Expression of foxp3 by cancer cells

ABSTRACT

The present invention relates to the treatment, diagnosis, and prophylaxis of cancer based on the expression of foxp3.

FIELD OF THE INVENTION

The present invention relates to the treatment, diagnosis, andprophylaxis of cancer based on the expression of foxp3 in cancer cells.

BACKGROUND OF THE INVENTION

FoxP3 is well-established as the “master gene” that regulates thedevelopment and function of CD4+CD25+ T regulatory (T_(reg)) cells.Generally, T_(reg) cells represent approximately 5% of the CD4+ T-cellsin human blood and are essential in maintaining immune homeostasis viaT_(reg) cell-mediated immune suppression, which may lead to tumor immuneescape.

The immune system is subject to many levels of control which, together,avert attack on self tissues and limit over-exuberant immune responsesto pathogens. In recent years, it has been recognized that distinctpopulations of T cells with ‘regulatory’ (or suppressor) function make amajor contribution to keeping the immune system in check (1, 2). Amongstthese, the best understood is the population of regulatory T cellscharacterized by constitutive expression of CD25 and the transcriptionfactor FoxP3 (3, 4). These cells, known as Treg, are primarily noted fortheir ability to block the proliferation and cytokine secretion capacityof other T cells. Suppression is dependent on direct contact with thetarget cell yet, despite extensive investigation, the primarysuppressive mechanisms involved are still unclear. Production ofimmunosuppressive cytokines such as TGF-β and expression of surfacemolecules such as CTLA-4 may play a role, but their relative importanceremains controversial (5).

Despite an essential role in preventing autoimmunity, Treg can also havea negative impact on health by down-regulating beneficial immuneresponses such as those mounted against tumors. Numerous studies inanimal models have demonstrated that specifically removing or inhibitingTreg dramatically improves tumor clearance and survival (6, 7).Furthermore, a number of reports have documented the presence of Tregwithin human tumor tissue, and in one of these studies the number ofTreg also showed a clear negative correlation with survival (6-10).Thus, Treg may play a major role in preventing the development ofeffective anti-tumor immunity.

FoxP3 is a member of the forkhead family of transcription factors and,at least in mice, appears to act as a ‘master switch’ for thedevelopment and function of Treg (4, 11). Mice lacking functionalexpression of FoxP3 completely lack Treg, a deficit which is thought tobe responsible for the fatal immunoproliferative disease these micedevelop. Moreover, ectopic expression of FoxP3 in conventional mouse Tcells endows them with the full phenotype and function of Treg. Inhumans, there is also a strong association between FoxP3 expression andthe Treg phenotype, although the relationship may not be as simple as inmice (11). Mutations in FOXP3 have been associated with the developmentof a multi-organ autoimmune disorder known as IPEX (immunedysregulation, polyendocrinopathy, enteropathy, X-linked syndrome) (12),suggesting that defects in FoxP3 expression or function lead to impairedTreg development. In keeping with this hypothesis, Treg from thesepatients have greatly reduced suppressive activity (13). Furthermore,ectopic expression of FoxP3 allows conventional human T cells to acquiremany characteristics of Treg, although some studies have shown thattheir suppressive activity is inferior to that of bona fide Treg (14,15). Interestingly, while expression of FoxP3 in freshly isolatedperipheral blood is limited to Treg, in vitro activation can lead to atransient expression of FoxP3 by conventional T cells; it is currently amatter of debate as to whether or not these cells have regulatoryactivity (16-18). Thus, whereas FoxP3 is both necessary and sufficientfor Treg activity in mice, other factors in addition to FoxP3 may beinvolved in induction of human Treg activity.

SUMMARY OF THE INVENTION

To date, FoxP3 expression has been thought to be restricted to the Tcell lineage (19, 20). In the present study, however, we provide severallines of evidence that—in addition to T cells—FoxP3 is also expressed bytumor cells. Given the central role of FoxP3 in Treg function, theexpression of FoxP3 by tumor cells may represent a novel mechanism bywhich cancers suppress the immune system in order to escape destruction.

We have observed for the first time that FoxP3 expression in tumortissue was not only restricted to the infiltrating T_(reg), but was alsoexpressed within the tumor cells Therefore, we hypothesized that theexpression of FoxP3 during tumorigenesis may result in tumorimmunological tolerance. We verified FoxP3 expression in a large numberof melanoma cell lines using flow cytometry, reverse-transcriptase PCRand Western blot. Furthermore, we extended the study with tumor celllines from other organs and demonstrated that the majority expressedFoxP3. In contrast, we showed that normal primary cell lines did notexpress FoxP3 supporting the association of FoxP3 expression withtumorigenesis. Meanwhile, we discovered a novel third splice isoform ofFoxP3 expressed specifically in the brain and reproductive organs,suggesting that these tissues may establish an immune privilege-likesite by expressing FoxP3. Our data reveal that tumor cells expressFoxP3, hence suggesting that the expression of FoxP3 by tumor cells iscrucial as a tool of survival through suppression of anti-tumor immuneresponses. Ultimately, identifying the origin of tumor evasion is astepping stone towards manipulating our immune system to eradicate tumorcells.

According to one aspect of the invention, methods for diagnosing cancerin a subject are provided. The methods include obtaining a biologicalsample from the subject, and determining the expression in thebiological sample of a FoxP3 polypeptide or a nucleic acid molecule thatencodes the FoxP3 polypeptide. The nucleic acid molecule preferablycomprises SEQ ID NO:1, or a nucleotide sequence that is at least 90%identical to the nucleotide sequence of SEQ ID NO:1. The expression inthe biological sample of the polypeptide or the nucleic acid moleculethat encodes it is indicative of the subject having cancer. The cancerpreferably is not pancreatic carcinoma. Preferably the biological sampleis free of regulatory T cells (T_(reg); CD4+CD25+FOXP3+).

In some embodiments the step of determining the expression of thepolypeptide or the nucleic acid molecule that encodes the polypeptideincludes contacting the biological sample with an agent that selectivelybinds to the polypeptide or the nucleic acid molecule that encodes thepolypeptide. In some embodiments the agent is a nucleic acid probe or anucleic acid primer. Preferably the expression of the nucleic acidmolecule is determined by nucleic acid hybridization using the nucleicacid probe or nucleic acid amplification using the nucleic acid primer.In some preferred embodiments the nucleic acid amplification isreal-time RT-PCR or RT-PCR. In other preferred embodiments the nucleicacid hybridization is performed using a nucleic acid microarraycontaining the nucleic acid probe.

In other embodiments the agent is a polypeptide, such as an antibody orantigen-binding fragment thereof, preferably a monoclonal antibody, or aF(ab′)₂, Fab, Fd, or Fv fragment. In some preferred embodiments theantibody or antigen-binding fragment is labeled with a detectable label,preferably a fluorescent or radioactive label.

In some of the foregoing methods, the sample comprises tissue, cells,and/or blood.

According to another aspect of the invention, methods for diagnosingcancer in a subject are provided. The methods include obtaining abiological sample from the subject, and determining the expression inthe biological sample of a FoxP3 polypeptide or a nucleic acid moleculethat encodes the FoxP3 polypeptide. The nucleic acid molecule comprises(1) SEQ ID NO:6, foxp3 (SEQ ID NO:1) lacking exons 2 and 3, or a nucleicacid molecule comprising foxp3 exons 1 and 4 joined together, or (2) anucleotide sequence that is at least 90% identical to the nucleotidesequence of (1). The expression in the biological sample of thepolypeptide or the nucleic acid molecule that encodes it is indicativeof the subject having cancer. Preferably the biological sample is freeof regulatory T cells (T_(reg); CD4+CD25+FOXP3+).

In some embodiments the step of determining the expression of thepolypeptide or the nucleic acid molecule that encodes the polypeptideincludes contacting the biological sample with an agent that selectivelybinds to the polypeptide or the nucleic acid molecule that encodes thepolypeptide. In some embodiments the agent is a nucleic acid probe or anucleic acid primer. Preferably the expression of the nucleic acidmolecule is determined by nucleic acid hybridization using the nucleicacid probe or nucleic acid amplification using the nucleic acid primer.In some preferred embodiments the nucleic acid amplification isreal-time RT-PCR or RT-PCR. In other preferred embodiments the nucleicacid hybridization is performed using a nucleic acid microarraycontaining the nucleic acid probe.

In other embodiments the agent is a polypeptide, such as an antibody orantigen-binding fragment thereof, preferably a monoclonal antibody, or aF(ab′)₂, Fab, Fd, or Fv fragment. In some preferred embodiments theantibody or antigen-binding fragment is labeled with a detectable label,preferably a fluorescent or radioactive label.

In some of the foregoing methods, the sample comprises tissue, cells,and/or blood.

According to another aspect of the invention, isolated nucleic acidmolecules are provided that are selected from the group consisting of:(a) complements of nucleic acid molecules that hybridize under highstringency conditions to a second nucleic acid molecule comprising anucleotide sequence set forth as SEQ ID NO:6, foxp3 (SEQ ID NO:1)lacking exons 2 and 3, or foxp3 exons 1 and 4 joined together, (b)nucleic acid molecules that differ from the nucleic acid molecules of(a) in codon sequence due to the degeneracy of the genetic code, and (c)full-length complements of (a) or (b).

In some embodiments the isolated nucleic acid molecule comprises orconsists of SEQ ID NO:6. In other embodiments the isolated nucleic acidmolecule comprises or consists of foxp3 (SEQ ID NO:1) lacking exons 2and 3. In still other embodiments the isolated nucleic acid moleculecomprises or consists of foxp3 exons 1 and 4 joined together.

According to another aspect of the invention, isolated nucleic acidmolecules are provided that include a nucleotide sequence that is atleast about 90% identical to a nucleotide sequence set forth as SEQ IDNO:6, foxp3 (SEQ ID NO:1) lacking exons 2 and 3, or foxp3 exons 1 and 4joined together, or a full-length complement thereof.

In some embodiments the nucleic acid molecule comprises a nucleotidesequence that is at least about 95% identical, preferably at least about97% identical, more preferably at least about 98% identical, still morepreferably at least about 99% identical.

Compositions that include the foregoing isolated nucleic acid moleculesand a carrier also are provided, as are compositions that include theforegoing isolated nucleic acid molecules attached to a solid substrate.

According to another aspect of the invention, kits are provided thatinclude one or more of the foregoing nucleic acid molecules thathybridize under high stringency conditions to the isolated foxp3 nucleicacid molecules. In some embodiments the one or more nucleic acidmolecules are detectably labeled. In other embodiments the one or morenucleic acid molecules consist of a first primer and a second primer,wherein the first primer and the second primer are constructed andarranged to selectively amplify at least a portion of a nucleic acidmolecule that comprises a nucleotide sequence set forth as SEQ ID NO:6,foxp3 (SEQ ID NO:1) lacking exons 2 and 3, or foxp3 exons 1 and 4 joinedtogether.

According to a further aspect of the invention, expression vectors thatinclude the foregoing isolated nucleic acid molecules operably linked toa promoter, and isolated host cells transformed or transfected withthese expression vectors also are provided.

According to additional aspects of the invention, isolated polypeptidesencoded by the foregoing isolated nucleic acid molecules or that includethe amino acid sequence of SEQ ID NO:11 are provided. The invention alsoprovides isolated antibodies or antigen-binding fragments thereof thatselectively binds to these isolated polypeptides. In some embodimentsthe antibody is a monoclonal antibody, a human antibody, a domainantibody, a humanized antibody, a single chain antibody or a chimericantibody. In other embodiments the antibody fragment is a F(ab′)₂, Fab,Fd, or Fv fragment. Compositions that include the isolated antibodies orantigen-binding fragments and a carrier also are provided, as are kitsthat include the isolated antibodies or antigen-binding fragments.

According to another aspect of the invention, siRNA molecules thatselectively target SEQ ID NO:6, foxp3 (SEQ ID NO:1) lacking exons 2 and3, or a nucleic acid molecule comprising foxp3 exons 1 and 4 joinedtogether are provided.

According to still another aspect of the invention, methods for treatingor preventing cancer are provided. The methods include administering toa subject in need of such treatment an agent that reduces expression ofFoxP3 nucleic acid or polypeptide in the subject, in an amount effectiveto treat or prevent cancer. Preferably the cancer is not pancreaticcarcinoma.

In some embodiments the agent is administered by intratumoraladministration. In preferred embodiments the agent is a siRNA moleculeor an antisense nucleic acid molecule. Preferably the agent selectivelytargets SEQ ID NO:6, foxp3 (SEQ ID NO:1) lacking exons 2 and 3, or anucleic acid molecule comprising foxp3 exons 1 and 4 joined together. Inother embodiments, the cancer is a B cell lymphoma.

According to yet a further aspect of the invention, methods for treatingor preventing cancer are provided. The methods include administering toa subject in need of such treatment an agent that reduces expression inthe subject of a nucleic acid molecule comprising SEQ ID NO:6, foxp3(SEQ ID NO:1) lacking exons 2 and 3, or a nucleic acid moleculecomprising foxp3 exons 1 and 4 joined together, in an amount effectiveto treat or prevent cancer.

In some embodiments the agent is administered by intratumoraladministration. In preferred embodiments the agent is a siRNA moleculeor an antisense nucleic acid molecule. Preferably the agent selectivelytargets SEQ ID NO:6, foxp3 (SEQ ID NO:1) lacking exons 2 and 3, or anucleic acid molecule comprising foxp3 exons 1 and 4 joined together. Inother embodiments, the cancer is a B cell lymphoma.

In a further aspect of the invention, methods for inducing an immuneresponse are provided. The methods include administering to a subject inneed of such treatment an agent that induces an immune response to aFoxP3 variant polypeptide lacking exons 2 and 3, in an amount effectiveto induce an immune response against the FoxP3 variant polypeptide. Insome embodiments, the agent is FoxP3 variant polypeptide lacking exons 2and 3, and/or a peptide comprising an epitope of the FoxP3 variantpolypeptide lacking exons 2 and 3. Preferred peptides include thepeptides as described in FIG. 12, which can be used singly or in anycombination. In some embodiments, the immune response is a CD4 and/or aCD8 response.

In further embodiments of the foregoing methods, the subject has acancer and the immune response is sufficient to treating or preventingcancer. In preferred methods, the cancer expresses the FoxP3 variantpolypeptide lacking exons 2 and 3, which can be detected using methodsdescribed herein and well known to persons skilled in the art. Incertain embodiments, the cancer is a B cell lymphoma.

According to another aspect of the invention, methods for inhibitingimmunological tolerance of tumors are provided. The methods includeadministering to a subject in need of such treatment an agent thatreduces expression of FoxP3 nucleic acid or polypeptide in the subject,in an amount effective to inhibit immunological tolerance of tumors.Preferably the cancer is not pancreatic carcinoma.

In some embodiments the agent is administered by intratumoraladministration. In preferred embodiments the agent is a siRNA moleculeor an antisense nucleic acid molecule. Preferably the agent selectivelytargets SEQ ID NO:6, foxp3 (SEQ ID NO:1) lacking exons 2 and 3, or anucleic acid molecule comprising foxp3 exons 1 and 4 joined together.

According to yet a further aspect of the invention, methods forinhibiting immunological tolerance of tumors are provided. The methodsinclude administering to a subject in need of such treatment an agentthat reduces expression in the subject of a nucleic acid moleculecomprising SEQ ID NO:6, foxp3 (SEQ ID NO:1) lacking exons 2 and 3, or anucleic acid molecule comprising foxp3 exons 1 and 4 joined together, inan amount effective to inhibit immunological tolerance of tumors.

In some embodiments the agent is administered by intratumoraladministration. In preferred embodiments the agent is a siRNA moleculeor an antisense nucleic acid molecule. Preferably the agent selectivelytargets SEQ ID NO:6, foxp3 (SEQ ID NO:1) lacking exons 2 and 3, or anucleic acid molecule comprising foxp3 exons 1 and 4 joined together.

According to another aspect of the invention, methods for treating orpreventing post-transplant lymphoproliferative disorder (PTLD) areprovided. The methods include administering to a subject in need of suchtreatment an agent that reduces expression of FoxP3 in the subject, inan amount effective to treat or prevent PTLD.

In some embodiments the agent is administered before, during and/orafter solid organ or bone marrow transplantation. In preferredembodiments the agent is a siRNA molecule or an antisense nucleic acidmolecule. Preferably the agent selectively targets SEQ ID NO:6, foxp3(SEQ ID NO:1) lacking exons 2 and 3, or a nucleic acid moleculecomprising foxp3 exons 1 and 4 joined together.

According to a further aspect of the invention, methods for treating orpreventing post-transplant lymphoproliferative disorder (PTLD) areprovided. The methods include administering to a subject in need of suchtreatment an agent that reduces expression in the subject of a nucleicacid molecule comprising SEQ ID NO:6, foxp3 (SEQ ID NO:1) lacking exons2 and 3, or a nucleic acid molecule comprising foxp3 exons 1 and 4joined together, in an amount effective to treat or prevent PTLD.

In some embodiments the agent is administered before, during and/orafter solid organ or bone marrow transplantation. In preferredembodiments the agent is a siRNA molecule or an antisense nucleic acidmolecule. Preferably the agent selectively targets SEQ ID NO:6, foxp3(SEQ ID NO:1) lacking exons 2 and 3, or a nucleic acid moleculecomprising foxp3 exons 1 and 4 joined together.

The use of the foregoing compositions in the preparation of medicamentsfor treatment of disease, particularly cancer, also is provided inaccordance with the invention.

These and other aspects of the invention, as well as various embodimentsthereof, will become more apparent in reference to the drawings anddetailed description of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: FoxP3 expression by lymphocytes and tumor cells in metastaticmelanoma tissue sections. (a); FoxP3 staining in cells with themorphology of lymphocytes (open arrows) or tumor cells (solid arrows) at10× magnification. An enlarged (300%) view of each cell type is shown inthe inset. (b); co-staining for FoxP3 (brown, nuclear) and Melan-A(pink, cytoplasmic) at 40× magnification.

FIG. 2: Detection of FoxP3 in metastatic melanoma tissue using flowcytometry. Cell suspensions were generated from metastatic melanomatumor tissue and stained for flow cytometric analysis. (a):representative analysis, showing hierarchical gating strategy foridentification of tumor cells and T cells. For each gated population,staining with anti-FoxP3 mAb or an isotype matched negative control isshown. Quadrant markers were set on the basis of isotype controlstaining, while the region indicated by the dotted line was set toidentify FoxP3^(bright) tumor cells. (b): A second sample (gated onCD3−CD4−CD31−CD90−), illustrating FoxP3 staining of the entire melanomacell population. (c): tumor cells were sorted from disagregated tumortissue and expression of mRNA for FOXP3, CD4 and the housekeeping geneCYP-A was assessed by RT-PCR. Peripheral blood CD4+ T cells are shownfor comparision. Expression of CD3 and MCSP was determined by flowcytometry after sorting to confirm that the FOXP3 transcripts did notoriginate from Treg (sample #1 is shown).

FIG. 3: FoxP3 is widely expressed in melanoma cell lines. (a-b): Cellswere stained using anti-FoxP3 mAb (solid line) or isotype-matchednegative control (broken line) and analysed by flow cytometry. In (a),one representative melanoma cell line (SK-Mel-14) is shown, togetherwith peripheral blood CD4+CD25+ T cells, NK cells and monocytes forcomparison. In (b), results for a panel of melanoma cell lines are shown(black bars), together with a range of negative controls (peripheralblood NK cells/monocytes, and 7-day cultured monocyte-derived DCs; greybars). For each sample, the MFI was determined following staining withanti-FoxP3 and isotype control and the ratio calculated. (c): Westernblot analysis of lysates prepared from a short-term expanded Treg cellline, two melanoma cell lines and peripheral blood NK cells.

FIG. 4: FoxP3 mRNA is expressed as 3 distinct isoforms in melanomacells. (a): RNA extracted from 1×10⁶ cells was reverse transcribed andthe cDNA amplified by PCR (35 cycles) using primers specific for FOXP3and CYP-A. Shown are representative melanoma cell lines andMACS-purified peripheral blood CD4+ T cells and NK cells. (b): FOXP3 PCRwas repeated at 40 cycles, to better visualize the third PCR product.Shown are 4 melanoma cell lines, MACS-purified peripheral blood CD4⁺ Tcells and a short-term expanded Treg cell line. (c): Sequence of theupper (608 bp; SEQ ID NO:4) and lower (364 bp; Δ2,3; SEQ ID NO:6) FOXP3PCR products. Primer sites are underlined. (d): Predicted amino acidsequence of the Δ⅔ isoform (SEQ ID NO:11), compared to the publishedprotein sequence for full-length FoxP3 (SEQ ID NO:12). For the Δ⅔isoform, the sequence in bold type differs from the wild type protein,and the premature stop codon is underlined.

FIG. 5: Expression of FoxP3 in cell lines derived from other types ofsolid tumor or normal fibroblasts. (a-b): tumor cell lines (a) andnormal fibroblast cultures (early and late passage; b) were analysed byflow cytometry. The mean fluorescence intensity (MFI) was determinedfollowing staining with anti-FoxP3 and isotype control and the ratiocalculated. The grey region indicates the background level as determinedin FIG. 3 b. (c): RNA extracted from 1×10⁶ cells was reverse transcribedand the cDNA amplified by PCR (35 cycles) using primers specific forFOXP3 and CYP-A. Shown are representative cell lines derived from thefollowing types of cancer: colon cancer (CaCo2), lung cancer (NCI-H460),breast cancer (MDA-MB-468), prostate cancer (PC3), glioblastoma (A172),renal cell carcinoma (SKRC09) and bladder cancer (5637); as well as CD4+T cells and NK cells purified from peripheral blood.

FIG. 6: De novo induction of FoxP3 expression during EBV transformationof B cells in vitro and in vivo. (a-c): PBMC from 4 healthy donors wereinfected with EBV in vitro and monitored for expression of FoxP3 by flowcytometry. After 30 days' culture, cells were gated into ‘smalllymphocyte’ and ‘blast’ populations on the basis of forward and sidescatter parameters (a), and the CD19+ B cells within each gate wereassessed for FoxP3 expression (solid line) compared to staining withisotype matched control mAb (broken line)(b). In (c), a full time-courseanalysis of all 4 donors is shown. The B cell blast population isdisplayed from the first time point at which it was clearly detectable(day 15) (d): Analysis of PBMC and tumor cells from a patient with PTLD.Cells were stained for CD19 and either isotype control or anti-FoxP3 asindicated. Analysis is gated on CD4-negative lymphocytes.

FIG. 7: FoxP3-expressing tumor cell lines suppress T cell proliferation.CD8⁺ T cells were purified from PBMC of a healthy donor, labeled withCFSE and activated with antibody-coated beads for 4 days in the presenceor absence of the indicated tumor cells or CD4⁺ CD25⁺ Treg (isolatedfrom a different donor). The percent suppression value for each tumorcell/Treg co-culture was calculated relative to T cells cultured in theabsence of suppressor cells, as described in Methods. In (a-b), T cellswere cultured in 96-well plates with titrated numbers of tumorcells/Treg. In (c-d), tumor cells were placed in the bottom chamber of a0.4 μm Transwell plate and T cells added to either the same chamber(‘co-culture’) or the upper chamber (‘separated’). Flow cytometryprofiles (b) and (c) show results for SK-Mel-14 at 2:1 tumor:T cellratio. All data are representative of two independent experiments withsimilar results.

FIG. 8 shows that PCR amplification of cDNA from brain and testis tissuereveals three distinct foxp3 isoforms.

FIG. 9 depicts immunohistochemical staining of normal adult testistissue for FoxP3 (FIG. 9A) and NY-ESO-1 (FIG. 9B).

FIG. 10 shows real-time PCR measurement of foxp3 gene expressionfollowing transfection with control (non-targeting) or foxp3-specificsiRNA constructs.

FIG. 11: Western blotting of melanoma cell line lysates using anantibody raised against the Δ3,4 variant. A polyclonal antiserum to a 15amino acid variant FoxP3 peptide (SSRERWYSLWSSSWC; SEQ ID NO:13) wasused at a final concentration of 2 μg/ml to probe lysates prepared fromthree different melanoma cell lines, all of which express the Δ3,4 FoxP3variant by RT-PCR (the Δ3,4 FoxP3 variant is also referred to as theΔ2,3 FoxP3 variant herein). Note that the predicted molecular weight ofthe variant is approximately 17 kD. FIG. 11 a demonstrates the presenceof a band of the expected size for all three melanoma cell lines tested.To demonstrate the specificity of the reaction, the antibody waspre-blocked for 2 hours at room temperature with either the peptide usedfor immunization or an irrelevant peptide control (0.2 μg/ml). Theantibody/peptide mixture was then used for Western blotting and banddensity was determined using ImageQuaNT software. This analysis is shownin FIG. 11 b, and demonstrates that the band intensity is greatlyreduced after blocking with the specific peptide.

FIG. 12: T cell responses to the Δ3,4 variant in a patient with advancedmelanoma. A panel of overlapping 18 amino acid peptides was synthesizedcovering the entire predicted protein sequence of the Δ3,4 variant.Patient peripheral blood mononuclear cells (PBMC) were cultured witheach peptide for 11 days in the presence of 25 IU/ml IL-2 and thenre-stimulated with the same peptide for 4 hours in the presence ofBrefeldin-A. The cells were then stained with fluorochrome-conjugatedantibodies to CD4 and CD8, fixed with 1% formaldehyde and incubatedovernight with FITC-conjugated anti-IFN-γ in the presence of 0.2%saponin. Cells were then subject to flow cytometric analysis, gating oneither CD8⁺ (FIG. 12 a) or CD4⁺ (FIG. 12 b) T cells.

DETAILED DESCRIPTION OF THE INVENTION

The invention relates in part to the discovery that FoxP3 polypeptidesand nucleic acid molecules that encode the FoxP3 polypeptides areexpressed in cancer cells and tumors. As used herein, the “nucleic acidmolecules that encode” means the nucleic acid molecules that code forthe FoxP3 polypeptides or fragments thereof, particularly immunogenicfragments. These nucleic acid molecules may be DNA or may be RNA (e.g.,mRNA). The FoxP3 nucleic acid molecules of the invention also encompassvariants of the nucleic acid molecules described herein. These variantsmay be splice variants, some of which are described herein for FoxP3, orallelic variants of certain sequences provided. Variants of the nucleicacid molecules of the invention are intended to include homologs andalleles which are described further below. Further, as used herein, theterm “FoxP3 molecules” includes FoxP3 polypeptides and fragments thereofas well as FoxP3 nucleic acids and fragments (such as exon sequences).In all embodiments, human FoxP3 polypeptides and the nucleic acidmolecules that encode them are preferred.

In one aspect, the invention provides isolated nucleic acid moleculesthat are splice variants of FoxP3 and may encode variant FoxP3polypeptides. The isolated nucleic acid molecules of this aspect of theinvention comprise: (a) nucleotide sequences set forth as or comprisingSEQ ID NO:6 or FoxP3 (SEQ ID NO:1) lacking exons 2 and 3 or FoxP3 exons1 and 4 joined together; (b) isolated nucleic acid molecules whichhybridize under highly stringent conditions to the nucleic acidmolecules of (a) and preferably which code for a FoxP3 polypeptide; (c)nucleic acid molecules that differ from (a) or (b) due to the degeneracyof the genetic code, and (d) full-length complements of (a), (b) or (c).

The novel FoxP3 splice variant is referred to herein primarily as Δ2,3.This nomenclature was developed on the basis of naming the first codingexon as exon 1. This is the convention commonly adopted within the FoxP3literature, and as such, the splice variant detected in Treg isgenerally referred to as Δ2 (38-40). However, there is an additionalexon upstream of the translation start site, and the Genbank entry forthe FOXP3 gene refers to this as exon 1 (see accession numberNM_(—)014009). Accordingly, the first coding exon is referred to as exon2. This alternative nomenclature has also been used in a recentpublication (27). Therefore, the splice variant detected in tumor cellsmay be referred to as Δ2, 3 or Δ3,4 herein.

As used herein the term “isolated nucleic acid molecule” means: (i)amplified in vitro by, for example, polymerase chain reaction (PCR);(ii) recombinantly produced by cloning; (iii) purified, as by cleavageand gel separation; or (iv) synthesized by, for example, chemicalsynthesis. An isolated nucleic acid is one which is readily manipulableby recombinant DNA techniques well known in the art. Thus, a nucleotidesequence contained in a vector in which 5′ and 3′ restriction sites areknown or for which polymerase chain reaction (PCR) primer sequences havebeen disclosed is considered isolated but a nucleic acid sequenceexisting in its native state in its natural host is not. An isolatednucleic acid may be substantially purified, but need not be. Forexample, a nucleic acid that is isolated within a cloning or expressionvector is not pure in that it may comprise only a small percentage ofthe material in the cell in which it resides. Such a nucleic acid isisolated, however, as the term is used herein because it is readilymanipulable by standard techniques known to those of ordinary skill inthe art.

The FoxP3 nucleic acid molecules of the invention also encompasshomologs and alleles which can be identified by conventional techniques.Identification of human and other organisms' homologs of FoxP3polypeptides will be familiar to those of skill in the art. In general,nucleic acid hybridization is a suitable method for identification ofhomologous sequences of another species (e.g., human, cow, sheep, dog,rat, mouse), which correspond to a known sequence. Standard nucleic acidhybridization procedures can be used to identify related nucleic acidsequences of selected percent identity. For example, one can construct alibrary of cDNAs reverse transcribed from the mRNA of a selected tissueand use the FoxP3 nucleic acid molecules identified herein to screen thelibrary for related nucleotide sequences. The screening preferably isperformed using high-stringency conditions to identify those sequencesthat are closely related by sequence identity. Nucleic acids soidentified can be translated into polypeptides and the polypeptides canbe tested for activity.

The term “high stringency” as used herein refers to parameters withwhich the art is familiar. Nucleic acid hybridization parameters may befound in references that compile such methods, e.g. Molecular Cloning: ALaboratory Manual, J. Sambrook, et al., eds., Second Edition, ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, orCurrent Protocols in Molecular Biology, F. M. Ausubel, et al., eds.,John Wiley & Sons, Inc., New York. More specifically, high-stringencyconditions, as used herein, refers, for example, to hybridization at 65°C. in hybridization buffer (3.5×SSC, 0.02% Ficoll, 0.02% polyvinylpyrrolidone, 0.02% Bovine Serum Albumin, 2.5 mM NaH₂PO₄ (pH7), 0.5% SDS,2 mM EDTA). SSC is 0.15M sodium chloride/0.015M sodium citrate, pH7; SDSis sodium dodecyl sulphate; and EDTA is ethylenediaminetetracetic acid.After hybridization, the membrane upon which the DNA is transferred iswashed, for example, in 2×SSC at room temperature and then at0.1-0.5×SSC/0.1×SDS at temperatures up to 68° C.

There are other conditions, reagents, and so forth that can be used,which result in a similar degree of stringency. The skilled artisan willbe familiar with such conditions, and thus they are not given here. Itwill be understood, however, that the skilled artisan will be able tomanipulate the conditions in a manner to permit the clear identificationof homologs and alleles of the FoxP3 nucleic acids of the invention(e.g., by using lower stringency conditions). The skilled artisan alsois familiar with the methodology for screening cells and libraries forexpression of such molecules, which then are routinely isolated,followed by isolation of the pertinent nucleic acid molecule andsequencing.

In general, homologs and alleles typically will share at least 90%nucleotide identity and/or amino acid identity to the sequences of FoxP3nucleic acids and polypeptides, respectively, in some instances willshare at least 95% nucleotide identity and/or amino acid identity, inother instances will share at least 97% nucleotide identity and/or aminoacid identity, in other instances will share at least 98% nucleotideidentity and/or amino acid identity, and in other instances will shareat least 99% nucleotide identity and/or amino acid identity. Thehomology can be calculated using various, publicly available softwaretools developed by NCBI (Bethesda, Md.) that can be obtained through theinternet. Exemplary tools include the BLAST system available from thewebsite of the National Center for Biotechnology Information (NCBI) atthe National Institutes of Health. Pairwise and ClustalW alignments(BLOSUM30 matrix setting) as well as Kyte-Doolittle hydropathic analysiscan be obtained using a number of sequence analysis software programs,such as the MacVector sequence analysis software (Accelrys SoftwareInc., San Diego, Calif.). Watson-Crick complements of the foregoingnucleic acids also are embraced by the invention.

In another aspect of the invention, nucleic acid molecules are providedwhich include unique fragments of the nucleotide sequences of theinvention and complements thereof. The invention, in a preferredembodiment, provides unique fragments of SEQ ID NO:6 or FoxP3 exons 1and 4 joined together and complements thereof. A unique fragment is onethat is a ‘signature’ for the larger nucleic acid. It, for example, islong enough to assure that its precise sequence is not found inmolecules outside of the nucleic acid molecules that encode the FoxP3polypeptides defined above. Those of ordinary skill in the art may applyno more than routine procedures to determine if a fragment is uniquewithin the human genome. In some instances the unique fragment is atleast about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,25, 30, 35, 40, 45, 50, 75, or 100 amino acids in length.

Unique fragments can be used as probes in Southern blot assays andmicroarray assays to identify such nucleic acid molecules, or can beused as probes in amplification assays such as those employing thepolymerase chain reaction (PCR), including, but not limited to reversetranscribed (RT)-PCR and RT-real-time PCR. As known to those skilled inthe art, large probes such as 200 nucleotides or more are preferred forcertain uses such as Southern blots, while smaller fragments will bepreferred for uses such as microarrays and PCR. Unique fragments alsocan be used to produce fusion proteins for generating antibodies ordetermining binding of the polypeptide fragments, or for generatingimmunoassay components. Likewise, unique fragments can be employed toproduce nonfused fragments of the FoxP3 polypeptides useful, forexample, in the preparation of antibodies and in immunoassays.

In screening for FoxP3 genes, a Southern blot may be performed using theforegoing conditions, together with a detectably labeled probe (e.g.radioactive or chemiluminescent probes). After washing the membrane towhich the DNA is finally transferred, the membrane can be placed againstX-ray film or analyzed using a phosphorimager device to detect theradioactive or chemiluminescent signal. In screening for the expressionof FoxP3 nucleic acids, Northern blot hybridizations using the foregoingconditions or microarrays can be performed on samples taken from cancerpatients or subjects suspected of having a condition characterized byabnormal cell proliferation or neoplasia. Amplification protocols suchas polymerase chain reaction using primers that hybridize to thesequences presented also can be used for detection of the FoxP3 genes orexpression thereof.

Identification of related sequences can also be achieved usingpolymerase chain reaction (PCR) and other amplification techniquessuitable for cloning related nucleic acid sequences. Again, nucleicacids are preferably amplified from a tissue-specific library (e.g.,testis, brain, cancer cells).

The invention also includes degenerate nucleic acids that includealternative codons to those present in the native materials. Forexample, serine residues are encoded by the codons TCA, AGT, TCC, TCG,TCT and AGC. Each of the six codons is equivalent for the purposes ofencoding a serine residue. Thus, it will be apparent to one of ordinaryskill in the art that any of the serine-encoding nucleotide triplets maybe employed to direct the protein synthesis apparatus, in vitro or invivo, to incorporate a serine residue into an elongating FoxP3polypeptide. Similarly, nucleotide sequence triplets which encode otheramino acid residues include, but are not limited to: CCA, CCC, CCG, andCCT (proline codons); CGA, CGC, CGG, CGT, AGA, and AGG (argininecodons); ACA, ACC, ACG, and ACT (threonine codons); AAC and AAT(asparagine codons); and ATA, ATC, and ATI′ (isoleucine codons). Otheramino acid residues may be encoded similarly by multiple nucleotidesequences. Thus, the invention embraces degenerate nucleic acids thatdiffer from the biologically isolated nucleic acids in codon sequencedue to the degeneracy of the genetic code.

The invention also provides modified nucleic acid molecules, whichinclude additions, substitutions and deletions of one or morenucleotides (preferably 1-20 nucleotides). In preferred embodiments,these modified nucleic acid molecules and/or the polypeptides theyencode retain at least one activity or function of the unmodifiednucleic acid molecule and/or the polypeptides, such as antigenicity,receptor binding, etc. In certain embodiments, the modified nucleic acidmolecules encode modified polypeptides, preferably polypeptides havingconservative amino acid substitutions as are described elsewhere herein.The modified nucleic acid molecules are structurally related to theunmodified nucleic acid molecules and in preferred embodiments aresufficiently structurally related to the unmodified nucleic acidmolecules so that the modified and unmodified nucleic acid moleculeshybridize under stringent conditions known to one of skill in the art.

For example, modified nucleic acid molecules that encode polypeptideshaving single amino acid changes can be prepared. Each of these nucleicacid molecules can have one, two or three nucleotide substitutionsexclusive of nucleotide changes corresponding to the degeneracy of thegenetic code as described herein. Likewise, modified nucleic acidmolecules that encode polypeptides having two amino acid changes can beprepared which have, e.g., 2-6 nucleotide changes. Numerous modifiednucleic acid molecules like these will be readily envisioned by one ofskill in the art, including for example, substitutions of nucleotides incodons encoding amino acids 2 and 3, 2 and 4, 2 and 5, 2 and 6, and soon.

In the foregoing example, each combination of two amino acids isincluded in the set of modified nucleic acid molecules, as well as allnucleotide substitutions which code for the amino acid substitutions.Additional nucleic acid molecules that encode polypeptides havingadditional substitutions (i.e., 3 or more), additions or deletions(e.g., by introduction of a stop codon or a splice site(s)) also can beprepared and are embraced by the invention as readily envisioned by oneof ordinary skill in the art. Any of the foregoing nucleic acids orpolypeptides can be tested by routine experimentation for retention ofactivity or structural relation to the nucleic acids and/or polypeptidesdisclosed herein. As used herein the terms: “deletion”, “addition”, and“substitution” mean deletion, addition, and substitution changes toabout 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more nucleic acids of asequence of the invention.

According to yet another aspect of the invention, an expression vectorcomprising any of the isolated nucleic acid molecules of the invention,preferably operably linked to a promoter is provided. In a relatedaspect, host cells transformed or transfected with such expressionvectors also are provided. As used herein, a “vector” may be any of anumber of nucleic acid molecules into which a desired sequence may beinserted by restriction and ligation for transport between differentgenetic environments or for expression in a host cell. Vectors aretypically composed of DNA although RNA vectors are also available.Vectors include, but are not limited to, plasmids, phagemids, and virusgenomes.

A cloning vector is one which is able to replicate in a host cell, andwhich is further characterized by one or more endonuclease restrictionsites at which the vector may be cut in a determinable fashion and intowhich a desired DNA sequence may be ligated such that the newrecombinant vector retains its ability to replicate in the host cell. Inthe case of plasmids, replication of the desired sequence may occur manytimes as the plasmid increases in copy number within the host bacteriumor just a single time per host before the host reproduces by mitosis. Inthe case of phage, replication may occur actively during a lytic phaseor passively during a lysogenic phase.

An expression vector is one into which a desired DNA sequence may beinserted by restriction and ligation such that it is operably joined toregulatory sequences and may be expressed as an RNA transcript.

Vectors may further contain one or more marker sequences suitable foruse in the identification of cells which have or have not beentransformed or transfected with the vector. Markers include, forexample, genes encoding proteins which increase or decrease eitherresistance or sensitivity to antibiotics or other compounds, genes whichencode enzymes whose activities are detectable by standard assays knownin the art, e.g., β-galactosidase or alkaline phosphatase, and geneswhich visibly affect the phenotype of transformed or transfected cells,hosts, colonies or plaques, e.g., green fluorescent protein. Preferredvectors are those capable of autonomous replication and expression ofthe structural gene products present in the DNA segments to which theyare operably joined.

As used herein, a coding sequence and regulatory sequences are said tobe “operably joined” when they are covalently linked in such a way as toplace the expression or transcription of the coding sequence under theinfluence or control of the regulatory sequences. As used herein,“operably joined” and “operably linked” are used interchangeably andshould be construed to have the same meaning. If it is desired that thecoding sequences be translated into a functional protein, two DNAsequences are said to be operably joined if induction of a promoter inthe 5′ regulatory sequences results in the transcription of the codingsequence and if the nature of the linkage between the two DNA sequencesdoes not (1) result in the introduction of a frame-shift mutation, (2)interfere with the ability of the promoter region to direct thetranscription of the coding sequences, or (3) interfere with the abilityof the corresponding RNA transcript to be translated into a protein.Thus, a promoter region is operably joined to a coding sequence if thepromoter region is capable of effecting transcription of that DNAsequence such that the resulting transcript can be translated into thedesired protein or polypeptide.

The precise nature of the regulatory sequences needed for geneexpression may vary between species or cell types, but shall in generalinclude, as necessary, 5′ non-transcribed and 5′ non-translatedsequences involved with the initiation of transcription and translationrespectively, such as a TATA box, capping sequence, CAAT sequence, andthe like. Often, such 5′ non-transcribed regulatory sequences willinclude a promoter region which includes a promoter sequence fortranscriptional control of the operably joined gene. Regulatorysequences may also include enhancer sequences or upstream activatorsequences as desired. The vectors of the invention may optionallyinclude 5′ leader or signal sequences. The choice and design of anappropriate vector is within the ability and discretion of one ofordinary skill in the art.

It will also be recognized that the invention embraces the use of theFoxP3 nucleic acid molecules and genomic sequences in expressionvectors, as well as to transfect host cells and cell lines, be theseprokaryotic, e.g., E. coli, or eukaryotic, e.g., CHO cells, COS cells,yeast expression systems, and recombinant baculovirus expression ininsect cells. Especially useful are mammalian cells such as human,mouse, hamster, pig, goat, primate, etc. They may be of a wide varietyof tissue types, including mast cells, fibroblasts, oocytes, andlymphocytes, and may be primary cells and cell lines. Specific examplesinclude dendritic cells, peripheral blood leukocytes, bone marrow stemcells and embryonic stem cells. The expression vectors require that thepertinent sequence, i.e., those nucleic acids described herein, beoperably linked to a promoter.

The invention, in one aspect, also permits the construction of FoxP3gene “knock-outs”, “knockdowns” and “knock-ins” in cells and in animals,providing materials for studying certain aspects of cancer and immunesystem responses to cancer.

Expression vectors containing all the necessary elements for expressionare commercially available and known to those skilled in the art. Cellsare genetically engineered by the introduction into the cells ofheterologous DNA or RNA encoding a FoxP3 polypeptide, a mutant FoxP3polypeptide, fragments, or variants thereof. The heterologous DNA or RNAis placed under operable control of transcriptional elements to permitthe expression of the heterologous DNA in the host cell.

Preferred systems for mRNA expression in mammalian cells are those suchas pcDNA3.1 and pCDM8 (Invitrogen) that contain a selectable marker(which facilitates the selection of stably transfected cell lines) andcontain the human cytomegalovirus (CMV) enhancer-promoter sequences.Additionally, suitable for expression in primate or canine cell lines isthe pCEP4 vector (Invitrogen), which contains an Epstein Barr virus(EBV) origin of replication, facilitating the maintenance of plasmid asa multicopy extrachromosomal element.

The invention also embraces kits termed expression kits, which allow theartisan to prepare a desired expression vector or vectors. Suchexpression kits include at least separate portions of each of thepreviously discussed coding sequences. Other components may be added, asdesired, as long as the previously mentioned sequences, which arerequired, are included.

The invention also includes kits for amplification of a FoxP3 nucleicacid, including at least one pair of amplification primers whichhybridize to a FoxP3 nucleic acid, preferably a FoxP3 nucleic acid inwhich exons 1 and 4 are joined, such as SEQ ID NO:6 or SEQ ID NO:1lacking exons 2 and 3. The primers preferably are about 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 or 32nucleotides in length and are non-overlapping to prevent formation of“primer-dimers”. One of the primers will hybridize to one strand of theFoxP3 nucleic acid and the second primer will hybridize to thecomplementary strand of the FoxP3 nucleic acid, in an arrangement thatpermits amplification of the FoxP3 nucleic acid. Selection ofappropriate primer pairs is standard in the art. For example, theselection can be made with assistance of a computer program designed forsuch a purpose, optionally followed by testing the primers foramplification specificity and efficiency.

The invention, in another aspect provides isolated polypeptides(including whole proteins and partial proteins) encoded by the foregoingFoxP3 nucleic acids, such as SEQ ID NO:11 (Δ⅔ isoform polypeptide) andSEQ ID NO:12 (full-length polypeptide). The amino acids of the inventionare also intended to encompass amino acid sequences that result from thetranslation of the nucleic acid sequences provided herein in a differentreading frame.

Such polypeptides are useful, for example, alone or as fusion proteinsto generate antibodies, and as components of an immunoassay ordiagnostic assay. Immunogenic FoxP3 polypeptides can be isolated frombiological samples including tissue or cell homogenates, and can also beexpressed recombinantly in a variety of prokaryotic and eukaryoticexpression systems by constructing an expression vector appropriate tothe expression system, introducing the expression vector into theexpression system, and isolating the recombinantly expressed protein.Fragments of the immunogenic FoxP3 polypeptides (including immunogenicpeptides) also can be synthesized chemically using well-establishedmethods of peptide synthesis. Thus, fragments of the disclosedpolypeptides are useful for eliciting an immune response.

Fragments of a polypeptide preferably are those fragments that retain adistinct functional capability of the polypeptide. Functionalcapabilities that can be retained in a fragment of a polypeptide includeinteraction with antibodies or MHC molecules (e.g. immunogenicfragments), interaction with other polypeptides or fragments thereof,selective binding of nucleic acids or proteins, and enzymatic activity.One important activity is the ability to provoke in a subject an immuneresponse. As will be recognized by those skilled in the art, the size ofthe fragment that can be used for inducing an immune response willdepend upon factors such as whether the epitope recognized by anantibody is a linear epitope or a conformational epitope or theparticular MHC molecule that binds to and presents the fragment (e.g.HLA class I or II). Thus, some immunogenic fragments of FoxP3polypeptides will consist of longer segments while others will consistof shorter segments, (e.g., about 5, 6, 7, 8, 9, 10, 11 or 12 or moreamino acids long, including each integer up to the full length of theFoxP3 polypeptide). Those skilled in the art are well versed in methodsfor selecting immunogenic fragments of polypeptides.

The invention embraces variants of the FoxP3 polypeptides describedabove. As used herein, a “variant” of a FoxP3 polypeptide is apolypeptide which contains one or more modifications to the primaryamino acid sequence of a FoxP3 polypeptide. Modifications which create aFoxP3 polypeptide variant can be made to a FoxP3 polypeptide 1) toreduce or eliminate an activity of a FoxP3 polypeptide; 2) to enhance aproperty of a FoxP3 polypeptide, such as protein stability in anexpression system or the stability of protein-protein binding; 3) toprovide a novel activity or property to a FoxP3 polypeptide, such asaddition of an antigenic epitope or addition of a detectable moiety; or4) to provide equivalent or better binding to a MHC molecule.

Modifications to a FoxP3 polypeptide are typically made to the nucleicacid which encodes the FoxP3 polypeptide, and can include deletions,point mutations, truncations, amino acid substitutions and additions ofamino acids or non-amino acid moieties. Alternatively, modifications canbe made directly to the polypeptide, such as by cleavage, addition of alinker molecule, addition of a detectable moiety, such as biotin,addition of a fatty acid, and the like. Modifications also embracefusion proteins comprising all or part of the FoxP3 polypeptide aminoacid sequence. One of skill in the art will be familiar with methods forpredicting the effect on protein conformation of a change in proteinsequence, and can thus “design” a variant FoxP3 polypeptide according toknown methods. One example of such a method is described by Dahiyat andMayo in Science 278:82-87, 1997, whereby proteins can be designed denovo. The method can be applied to a known protein to vary a only aportion of the polypeptide sequence. By applying the computationalmethods of Dahiyat and Mayo, specific variants of a FoxP3 polypeptidecan be proposed and tested to determine whether the variant retains adesired conformation.

In general, variants include FoxP3 polypeptides which are modifiedspecifically to alter a feature of the polypeptide unrelated to itsdesired physiological activity. For example, cysteine residues can besubstituted or deleted to prevent unwanted disulfide linkages.Similarly, certain amino acids can be changed to enhance expression of aFoxP3 polypeptide by eliminating proteolysis by proteases in anexpression system (e.g., dibasic amino acid residues in yeast expressionsystems in which KEX2 protease activity is present).

Mutations of a nucleic acid which encode a FoxP3 polypeptide preferablypreserve the amino acid reading frame of the coding sequence, andpreferably do not create regions in the nucleic acid which are likely tohybridize to form secondary structures, such a hairpins or loops, whichcan be deleterious to expression of the variant polypeptide.

Mutations can be made by selecting an amino acid substitution, or byrandom mutagenesis of a selected site in a nucleic acid which encodesthe polypeptide. Variant polypeptides are then expressed and tested forone or more activities to determine which mutation provides a variantpolypeptide with the desired properties. Further mutations can be madeto variants (or to non-variant FoxP3 polypeptides) which are silent asto the amino acid sequence of the polypeptide, but which providepreferred codons for translation in a particular host. The preferredcodons for translation of a nucleic acid in, e.g., E. coli, are wellknown to those of ordinary skill in the art. Still other mutations canbe made to the noncoding sequences of a FoxP3 gene or cDNA clone toenhance expression of the polypeptide. The activity of variants of FoxP3polypeptides can be tested by cloning the gene encoding the variantFoxP3 polypeptide into a bacterial or mammalian expression vector,introducing the vector into an appropriate host cell, expressing thevariant FoxP3 polypeptide; and testing for a functional capability ofthe FoxP3 polypeptides, as will be known to one of ordinary skill in theart.

The skilled artisan will also realize that conservative amino acidsubstitutions may be made in immunogenic FoxP3 polypeptides to providefunctionally equivalent variants, or homologs of the foregoingpolypeptides, i.e., the variants retain the functional capabilities ofthe immunogenic FoxP3 polypeptides. As used herein, a “conservativeamino acid substitution” refers to an amino acid substitution that doesnot alter the relative charge or size characteristics of the protein inwhich the amino acid substitution is made. Variants can be preparedaccording to methods for altering polypeptide sequence known to one ofordinary skill in the art such as are found in references that compilesuch methods, e.g. Molecular Cloning: A Laboratory Manual, J. Sambrook,et al., eds., Second Edition, Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y., 1989, or Current Protocols in Molecular Biology, F.M. Ausubel, et al., eds., John Wiley & Sons, Inc., New York. Exemplaryfunctionally equivalent variants or homologs of the FoxP3 polypeptidesinclude conservative amino acid substitutions of in the amino acidsequences of proteins disclosed herein. Conservative substitutions ofamino acids include substitutions made amongst amino acids within thefollowing groups: (a) M, I, L, V; (b) F, Y, W; (c) K, R, H; (d) A, G;(e) S, T; (f) Q, N; and (g) E, D. Therefore, one can make conservativeamino acid substitutions to the amino acid sequence of the FoxP3polypeptides disclosed herein and retain the specific antibody-bindingcharacteristics of the antigens.

Likewise, upon determining that a peptide derived from a FoxP3polypeptide is presented by an MHC molecule and recognized by antibodiesor T lymphocytes (e.g., helper T cells or CTLs), one can makeconservative amino acid substitutions to the amino acid sequence of thepeptide, particularly at residues which are thought not to be directcontact points with the MHC molecule. For example, methods foridentifying functional variants of HLA class II binding peptides areprovided in a published PCT application of Strominger and Wucherpfennig(PCT/US96/03182). Peptides bearing one or more amino acid substitutionsalso can be tested for concordance with known HLA/MHC motifs prior tosynthesis using, e.g. the computer program described by D′Amaro andDrijfhout (D'Amaro et al., Human Immunol. 43:13-18, 1995; Drijfhout etal., Human Immunol. 43:1-12, 1995). The substituted peptides can then betested for binding to the MHC molecule and recognition by antibodies orT lymphocytes when bound to MHC. These variants can be tested forimproved stability and are useful, inter alia, in vaccine compositions.

Conservative amino-acid substitutions in the amino acid sequence ofFoxP3 polypeptides to produce functionally equivalent variants of FoxP3polypeptides typically are made by alteration of a nucleic acid encodinga FoxP3 polypeptide. Such substitutions can be made by a variety ofmethods known to one of ordinary skill in the art. For example, aminoacid substitutions may be made by PCR-directed mutation, site-directedmutagenesis, or by chemical synthesis of a gene encoding a FoxP3polypeptide. Where amino acid substitutions are made to a small uniquefragment of a FoxP3 polypeptide, such as an antigenic epitope recognizedby autologous or allogeneic sera or T lymphocytes, the substitutions canbe made by directly synthesizing the peptide. The activity offunctionally equivalent variants of FoxP3 polypeptides can be tested bycloning the gene encoding the altered FoxP3 polypeptide into a bacterialor mammalian expression vector, introducing the vector into anappropriate host cell, expressing the altered polypeptide, and testingfor a functional capability of the FoxP3 polypeptides as disclosedherein. Peptides that are chemically synthesized can be tested directlyfor function, e.g., for binding to antisera recognizing associatedantigens.

The invention as described herein has a number of uses, some of whichare described elsewhere herein. In one aspect of the invention a methoddiagnosing cancer is provided, in which the expression of FoxP3 nucleicacids or polypeptides is indicative of and diagnostic for cancer. FoxP3nucleic acids or polypeptides can be identified by obtaining abiological sample from a subject. In another aspect, methods fortreating or preventing cancer are provided. Cancer can be treated byreducing the expression of FoxP3 nucleic acids or polypeptides.

As used herein, a “subject” is preferably a human, non-human primate,cow, horse, pig, sheep, goat, dog, cat or rodent. In all embodiments,human subjects are preferred. In some embodiments, the subject issuspected of having cancer or has been diagnosed with cancer. Cancers inwhich the FoxP3 nucleic acid or polypeptide are expressed includemelanoma, bladder cancer, prostate cancer, breast cancer, colon cancer,lung cancer, glioblastoma and renal cell carcinoma.

As used herein, a biological sample includes, but is not limited to:tissue, cells, and/or body fluid (e.g., serum, blood, lymph node fluid,etc.). The fluid sample may include cells and/or fluid. The tissue andcells may be obtained from a subject or may be grown in culture (e.g.,from a cell line). As used herein, a biological sample is body fluid,tissue or cells obtained from a subject using methods well-known tothose of ordinary skill in the related medical arts. The biologicalsample can include tumor tissue or cells, normal tissue or cells, to orcombinations thereof. In some embodiments, the biological sample istreated to remove T regulatory cells.

Thus determining the expression of FoxP3 polypeptides or nucleic acidmolecules in a biological sample of a subject can be used to diagnosewhether the subject has cancer.

Measurement of the expression of FoxP3 polypeptides or nucleic acidmolecules over time by sequential determinations permits monitoring ofthe disease and/or the effects of a course of treatment. For example, asample, such as serum, blood, or lymph node fluid, may be obtained froma subject, tested for expression of FoxP3 molecules, and at a second,subsequent time, another sample may be obtained from the subject andsimilarly tested. The results of the first and second (or subsequent)tests can be compared as a measure of the onset, regression orprogression of cancer, or, if cancer treatment was undertaken during theinterval between obtaining the samples, the effectiveness of thetreatment may be evaluated by comparing the results of the two tests.Other methods will be apparent to one of skill in the art.

Diagnostic methods of the invention involve determining the expressionof one or more of the FoxP3 polypeptides or the nucleic acid moleculesthat encode them, as described herein. Such determinations can becarried out via any standard nucleic acid assay, including thepolymerase chain reaction or assaying with hybridization probes, whichmay be labeled, or by assaying biological samples with binding partners(e.g., antibodies) for FoxP3 polypeptides.

The diagnostic methods of the invention can be used to detect thepresence of a disorder associated with aberrant expression of a FoxP3molecule (e.g., onset of the disorder), as well as to assess theprogression and/or regression of the disorder such as in response totreatment (e.g., chemotherapy, radiation). According to this aspect ofthe invention, the method for diagnosing a disorder characterized byaberrant expression of a FoxP3 molecule involve: detecting expression ofa FoxP3 molecule in a first biological sample obtained from a subject,wherein differential expression of the FoxP3 molecule compared to acontrol sample indicates that the subject has a disorder characterizedby aberrant expression of a FoxP3 molecule, such as cancer.

As described herein, FoxP3 molecules are expressed in testis tissue andcertain other normal tissues (brain, fetal brain, T_(reg) cells).Therefore, in all of the diagnostic methods described herein, thebiological sample preferably does not contain testis, brain or T_(reg)cells or tissue in order to avoid false-positive results.

As used herein, “aberrant expression” of a FoxP3 molecule is intended toinclude any expression that is statistically significant different fromthe expected (e.g., normal or baseline) amount of expression. Forexample, expression of a FoxP3 molecule (i.e., FoxP3 polypeptides or thenucleic acid molecules that encode them) in a tissue that is notexpected to express the FoxP3 molecule would be included in thedefinition of “aberrant expression”. Likewise, expression of the FoxP3molecule that is determined to be expressed at a significantly higher orlower level than expected is also included. Therefore, a determinationof the level of expression of one or more of the FoxP3 polypeptidesand/or the nucleic acids that encode them is diagnostic of cancer if thelevel of expression is above a baseline level determined for that tissuetype. The baseline level of expression can be determined using standardmethods known to those of skill in the art. Such methods include, forexample, assaying a number of histologically normal tissue samples(preferably not testis) from subjects that are clinically normal (i.e.do not have clinical signs of cancer in that tissue type) anddetermining the mean level of expression for the samples.

The level of expression of the nucleic acid molecules of the inventionor the polypeptides they encode can indicate cancer in the tissue whenthe level of expression is significantly more in the tissue than in acontrol sample. In some embodiments, a level of expression in thetissues that is at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%,80%, 90%, 100%, 150%, 200%, 250%, 300%, 400%, or 500% more than thelevel of expression in the control tissue indicates cancer in thetissue.

As used herein the term “control” means predetermined values, and alsomeans samples of materials tested in parallel with the experimentalmaterials. Examples include samples from control populations, biopsysamples taken from tissue adjacent to a biopsy sample suspected of beingcancerous and control samples generated through manufacture to be testedin parallel with the experimental samples.

As used herein the term “control” includes positive and negativecontrols which may be a predetermined value that can take a variety offorms. The control(s) can be a single cut-off value, such as a median ormean, or can be established based upon comparative groups, such as ingroups having normal amounts of FoxP3 molecules of the invention andgroups having abnormal amounts of FoxP3 molecules of the invention.Another example of a comparative group is a group having a particulardisease, condition and/or symptoms and a group without the disease,condition and/or symptoms. Another comparative group is a group with afamily history of a particular disease and a group without such a familyhistory of the particular disease. The predetermined control value canbe arranged, for example, where a tested population is divided equally(or unequally) into groups, such as a low-risk group, a medium-riskgroup and a high-risk group or into quadrants or quintiles, the lowestquadrant or quintile being individuals with the lowest risk or lowestexpression levels of a FoxP3 molecule of the invention that isup-regulated in cancer and the highest quadrant or quintile beingindividuals with the highest risk or highest expression levels of aFoxP3 molecule of the invention that is up-regulated in cancer.

The predetermined value of a control will depend upon the particularpopulation selected. For example, an apparently healthy population willhave a different “normal” FoxP3 molecule expression level range thanwill a population which is known to have a condition characterized byaberrant expression of the FoxP3 molecule, e.g., cancer. Accordingly,the predetermined value selected may take into account the category inwhich an individual falls. Appropriate ranges and categories can beselected with no more than routine experimentation by those of ordinaryskill in the art. Typically the control will be based on apparentlyhealthy individuals in an appropriate age bracket. As used herein, theterm “increased expression” means a higher level of expression relativeto a selected control.

The invention involves in some aspects diagnosing or monitoring cancerby determining the level of expression of one or more FoxP3 nucleic acidmolecules and/or determining the level of expression of one or moreFoxP3 polypeptides they encode. In some important embodiments, thisdetermination is performed by assaying a tissue sample from a subjectfor the level of expression of one or more FoxP3 nucleic acid moleculesor for the level of expression of one or more FoxP3 polypeptides encodedby the nucleic acid molecules of the invention. Preferred FoxP3 nucleicacid molecules include those in which exons 1 and 4 are joined, such asnucleic acids that include SEQ ID NO:6 or SEQ ID NO:1 lacking exons 2and 3.

The expression of the molecules of the invention may be determined usingroutine methods known to those of ordinary skill in the art. Thesemethods include, but are not limited to: direct RNA amplification,reverse transcription of RNA to cDNA, real-time RT-PCR, amplification ofcDNA, hybridization, and immunologically based assay methods, whichinclude, but are not limited to immunohistochemistry, antibody sandwichcapture assay, ELISA, and enzyme-linked immunospot assay (EliSpotassay). For example, the determination of the presence of level ofnucleic acid molecules of the invention in a subject or tissue can becarried out via any standard nucleic acid determination assay, includingthe polymerase chain reaction, or assaying with labeled hybridizationprobes. Such hybridization methods include, but are not limited tomicroarray techniques.

These methods of determining the presence and/or level of the moleculesof the invention in cells and tissues may include use of labels tomonitor the presence of the molecules of the invention. Such labels mayinclude, but are not limited to, radiolabels or chemiluminescent labels,which may be utilized to determine whether a molecule of the inventionis expressed in a cell or tissue, and to determine the level ofexpression in the cell or tissue. For example, a fluorescently labeledor radiolabeled antibody that selectively binds to a polypeptide of theinvention may be contacted with a tissue or cell to visualize thepolypeptide in vitro or in vivo. These and other in vitro and in vivoimaging methods for determining the presence of the nucleic acid andpolypeptide molecules of the invention are well known to those ofordinary skill in the art.

The invention also involves the use of agents such as polypeptides thatbind to FoxP3 polypeptides. Such agents can be used in methods of theinvention including the diagnosis and/or treatment of cancer. Suchbinding agents can be used, for example, in screening assays to detectthe presence or absence of FoxP3 polypeptides and can be used inquantitative binding assays to determine levels of expression inbiological samples and cells. Such agents also may be used to inhibitthe native activity of the FoxP3 polypeptides, for example, by bindingto such polypeptides.

According to this aspect, the binding polypeptides bind to an isolatednucleic acid or protein of the invention, including the novel splicevariant (SEQ ID NO:6) and unique fragments thereof. Preferably, thebinding polypeptides bind to a FoxP3 polypeptide, or a unique fragmentthereof.

In preferred embodiments, the binding polypeptide is an antibody orantibody fragment, such as an Fab or F(ab)₂ fragment of an antibody.Typically, the fragment includes a CDR3 region that is selective for theFoxP3 polypeptide. Any of the various types of antibodies can be usedfor this purpose, including polyclonal antibodies, monoclonalantibodies, humanized antibodies, and chimeric antibodies.

Thus, the invention provides agents which bind to FoxP3 polypeptidesencoded by FoxP3 nucleic acid molecules of the invention, and in certainembodiments preferably to unique fragments of the FoxP3 polypeptides.Such binding partners can be used in screening assays to detect thepresence or absence of a FoxP3 polypeptide and in purification protocolsto isolate such FoxP3 polypeptides. Likewise, such binding partners canbe used to selectively target drugs, toxins or other molecules(including detectable diagnostic molecules) to cells which express FoxP3polypeptides. In this manner, for example, cells present in solid ornon-solid tumors which express FoxP3 polypeptides can be treated withcytotoxic compounds that are selective for the FoxP3 molecules (nucleicacids and/or antigens). Such binding agents also can be used to inhibitthe native activity of the FoxP3 polypeptide, for example, to furthercharacterize the functions of these molecules.

The antibodies of the present invention thus are prepared by any of avariety of methods, including administering a protein, fragments of aprotein, cells expressing the protein or fragments thereof and the liketo an animal to induce polyclonal antibodies. The present invention alsoprovides methods of producing monoclonal antibodies to the FoxP3molecules of the invention described herein. The production ofmonoclonal antibodies is performed according to techniques well known inthe art. As detailed herein, such antibodies may be used for example toidentify tissues expressing protein or to purify protein. Antibodiesalso may be coupled to specific labeling agents or imaging agents,including, but not limited to a molecule preferably selected from thegroup consisting of fluorescent, enzyme, radioactive, metallic, biotin,chemiluminescent, bioluminescent, chromophore, or colored, etc. In someaspects of the invention, a label may be a combination of the foregoingmolecule types.

Significantly, as is well-known in the art, only a small portion of anantibody molecule, the paratope, is involved in the binding of theantibody to its epitope (see, in general, Clark, W. R. (1986) TheExperimental Foundations of Modern Immunology Wiley & Sons, Inc., NewYork; Roitt, I. (1991) Essential Immunology, 7th Ed., BlackwellScientific Publications, Oxford). The pFc′ and Fc regions, for example,are effectors of the complement cascade but are not involved in antigenbinding. An antibody from which the pFc′ region has been enzymaticallycleaved, or which has been produced without the pFc′ region, designatedan F(ab′)₂ fragment, retains both of the antigen binding sites of anintact antibody. Similarly, an antibody from which the Fc region hasbeen enzymatically cleaved, or which has been produced without the Fcregion, designated an Fab fragment, retains one of the antigen bindingsites of an intact antibody molecule. Fab fragments consist of acovalently bound antibody light chain and a portion of the antibodyheavy chain denoted Fd. The Fd fragments are the major determinant ofantibody specificity (a single Fd fragment may be associated with up toten different light chains without altering antibody specificity) and Fdfragments retain epitope-binding ability in isolation.

Within the antigen-binding portion of an antibody, as is well-known inthe art, there are complementarity determining regions (CDRs), whichdirectly interact with the epitope of the antigen, and framework regions(FRs), which maintain the tertiary structure of the paratope (see, ingeneral, Clark, 1986; Roitt, 1991). In both the heavy chain Fd fragmentand the light chain of IgG immunoglobulins, there are four frameworkregions (FR1 through FR4) separated respectively by threecomplementarity determining regions (CDR1 through CDR3): The CDRs, andin particular the CDR3 regions, and more particularly the heavy chainCDR3, are largely responsible for antibody specificity.

It is now well-established in the art that the non-CDR regions of amammalian antibody may be replaced with similar regions of nonspecificor heterospecific antibodies while retaining the epitopic specificity ofthe original antibody. This is most clearly manifested in thedevelopment and use of “humanized” antibodies in which non-human CDRsare covalently joined to human FR and/or Fc/pFc′ regions to produce afunctional antibody. See, e.g., U.S. Pat. Nos. 4,816,567, 5,225,539,5,585,089, 5,693,762, and 5,859,205.

Fully human monoclonal antibodies also can be prepared by immunizingmice transgenic for large portions of human immunoglobulin heavy andlight chain loci. Following immunization of these mice (e.g., XenoMouse(Abgenix), HuMAb mice (Medarex/GenPharm)), monoclonal antibodies can beprepared according to standard hybridoma technology. These monoclonalantibodies will have human immunoglobulin amino acid sequences andtherefore will not provoke human anti-mouse antibody (HAMA) responseswhen administered to humans.

Thus, as will be apparent to one of ordinary skill in the art, thepresent invention also provides for F(ab′)₂, Fab, Fv, and Fd fragments;chimeric antibodies in which the Fc and/or FR and/or CDR1 and/or CDR2and/or light chain CDR3 regions have been replaced by homologous humanor non-human sequences; chimeric F(ab′)₂ fragment antibodies in whichthe FR and/or CDR1 and/or CDR2 and/or light chain CDR3 regions have beenreplaced by homologous human or non-human sequences; chimeric Fabfragment antibodies in which the FR and/or CDR1 and/or CDR2 and/or lightchain CDR3 regions have been replaced by homologous human or non-humansequences; and chimeric Fd fragment antibodies in which the FR and/orCDR1 and/or CDR2 regions have been replaced by homologous human ornon-human sequences. The present invention also includes so-calledsingle chain antibodies, domain antibodies and heavy chain antibodies(Ablynx Nev., Ghent, Belgium).

Thus, the invention involves polypeptides of numerous size and type thatbind specifically to FoxP3 polypeptides. These polypeptides may bederived also from sources other than antibody technology. For example,such polypeptide binding agents can be provided by degenerate peptidelibraries which can be readily prepared in solution, in immobilized formor as phage display libraries. Combinatorial libraries also can besynthesized of peptides containing one or more amino acids. Librariesfurther can be synthesized of peptides and non-peptide syntheticmoieties.

The FoxP3 polypeptides of the invention can be used to screen peptidelibraries, including phage display libraries, to identify and selectpeptide binding partners of the FoxP3 molecules of the invention. Suchmolecules can be used, as described, for screening assays, fordiagnostic assays, for purification protocols or for targeting drugs,toxins and/or labeling agents (e.g., radioisotopes, fluorescentmolecules, etc.) to cells which express FoxP3 molecules such as cancercells which have aberrant FoxP3 expression.

Phage display can be particularly effective in identifying bindingpeptides useful according to the invention. Briefly, one prepares aphage library (using e.g. m13, fd, or lambda phage), displaying insertsfrom 4 to about 80 amino acid residues using conventional procedures.The inserts may represent, for example, a completely degenerate orbiased array. One then can select phage-bearing inserts which bind tothe FoxP3 polypeptide. This process can be repeated through severalcycles of reselection of phage that bind to the FoxP3 polypeptide.Repeated rounds lead to enrichment of phage bearing particularsequences. DNA sequence analysis can be conducted to identify thesequences of the expressed polypeptides. The minimal linear portion ofthe sequence that binds to the FoxP3 polypeptide can be determined. Onecan repeat the procedure using a biased library containing insertscontaining part or all of the minimal linear portion plus one or moreadditional degenerate residues upstream or downstream thereof. Yeasttwo-hybrid screening methods also may be used to identify polypeptidesthat bind to the FoxP3 polypeptides.

As detailed herein, the foregoing antibodies and other binding moleculesmay be used to identify tissues with normal or aberrant expression of aFoxP3 polypeptide. Antibodies also may be coupled to specific diagnosticlabeling agents for imaging of cells and tissues with normal or aberrantFoxP3 polypeptide expression or to therapeutically useful agentsaccording to standard coupling procedures. As used herein,“therapeutically useful agents” include any therapeutic molecule whichdesirably is targeted selectively to a cell or tissue selectively withan aberrant FoxP3 expression.

Diagnostic agents for in vivo use include, but are not limited to,barium sulfate, iocetamic acid, iopanoic acid, ipodate calcium,diatrizoate sodium, diatrizoate meglumine, metrizamide, tyropanoatesodium and radiodiagnostics including positron emitters such asfluorine-18 and carbon-11, gamma emitters such as iodine-123,technitium-99, iodine-131 and indium-111, and nuclides for nuclearmagnetic resonance such as fluorine and gadolinium. Other diagnosticagents useful in the invention will be apparent to one of ordinary skillin the art.

The antibodies of the present invention can also be used totherapeutically target FoxP3 polypeptides. In one embodiment, antibodiescan be used to target FoxP3 antigens expressed on the cell surface, suchas FoxP3 peptides presented by MHC molecules. This can be accomplished,for example, by raising antibodies that recognize the complex of FoxP3peptides and MHC molecules.

These antibodies can be linked not only to a detectable marker but alsoan antitumor agent or an immunomodulator. Antitumor agents can includecytotoxic agents and agents that act on tumor neovasculature. Detectablemarkers include, for example, radioactive or fluorescent markers.Cytotoxic agents include cytotoxic radionuclides, chemical toxins andprotein toxins.

The cytotoxic radionuclide or radiotherapeutic isotope preferably is analpha-emitting isotope such as ²²⁵Ac, ²¹¹At, ²¹²Bi, ²¹³Bi, ²¹²Pb, ²²⁴Raor ²²³Ra. Alternatively, the cytotoxic radionuclide may a beta-emittingisotope such as ¹⁸⁶Rh, ¹⁸⁸Rh, ¹⁷⁷Lu, ⁹⁰Y, ¹³¹I, ⁶⁷Cu, ⁶⁴Cu, ¹⁵³Sm or¹⁶⁶Ho. Further, the cytotoxic radionuclide may emit Auger and low energyelectrons and include the isotopes ¹²⁵I, ¹²³I or ⁷⁷Br.

Suitable chemical toxins or chemotherapeutic agents include members ofthe enediyne family of molecules, such as calicheamicin and esperamicin.Chemical toxins can also be taken from the group consisting ofmethotrexate, doxorubicin, melphalan, chlorambucil, ARA-C, vindesine,mitomycin C, cis-platinum, etoposide, bleomycin and 5-fluorouracil.Other antineoplastic agents that may be conjugated to the antibodies ofthe present invention include dolastatins (U.S. Pat. Nos. 6,034,065 and6,239,104) and derivatives thereof. Of particular interest is dolastatin10 (dolavaline-valine-dolaisoleuine-dolaproine-dolaphenine) and thederivatives auristatin PHE(dolavaline-valine-dolaisoleuine-dolaproine-phenylalanine-methyl ester)(Pettit, G. R. et al., Anticancer Drug Des. 13(4):243-277, 1998; Woyke,T. et al., Antimicrob. Agents Chemother. 45(12):3580-3584, 2001), andaurastatin E and the like. Toxins that are less preferred in thecompositions and methods of the invention include poisonous lectins,plant toxins such as ricin, abrin, modeccin, botulinum and diphtheriatoxins. Of course, combinations of the various toxins could also becoupled to one antibody molecule thereby accommodating variablecytotoxicity. Other chemotherapeutic agents are known to those skilledin the art.

Agents that act on the tumor vasculature can include tubulin-bindingagents such as combrestatin A4 (Griggs et al., Lancet Oncol. 2:82,2001), angiostatin and endostatin (reviewed in Rosen, Oncologist 5:20,2000, incorporated by reference herein) and interferon inducible protein10 (U.S. Pat. No. 5,994,292). A number of antiangiogenic agentscurrently in clinical trials are also contemplated. Agents currently inclinical trials include: 2ME2, Angiostatin, Angiozyme, Anti-VEGF RhuMAb,Apra (CT-2584), Avicine, Benefin, BMS275291, Carboxyamidotriazole,CC4047, CC5013, CC7085, CDC801, CGP-41251 (PKC 412), CM101,Combretastatin A-4 Prodrug, EMD 121974, Endostatin, Flavopiridol,Genistein (GCP), Green Tea Extract, IM-862, ImmTher, Interferon alpha,Interleukin-12, Iressa (ZD1839), Marimastat, Metastat (Col-3),Neovastat, Octreotide, Paclitaxel, Penicillamine, Photofrin, Photopoint,PI-88, Prinomastat (AG-3340), PTK787 (ZK22584), RO317453, Solimastat,Squalamine, SU 101, SU 5416, SU-6668, Suradista (FCE 26644), Suramin(Metaret), Tetrathiomolybdate, Thalidomide, TNP-470 and Vitaxin.additional antiangiogenic agents are described by Kerbel, J. Clin.Oncol. 19(18s):45s-51s, 2001, which is incorporated by reference herein.Immunomodulators suitable for conjugation to the antibodies includeα-interferon, γ-interferon, and tumor necrosis factor alpha (TNFα).

The coupling of one or more toxin molecules to the antibody isenvisioned to include many chemical mechanisms, for instance covalentbinding, affinity binding, intercalation, coordinate binding, andcomplexation. The toxic compounds used to prepare the immunotoxins areattached to the antibodies or antigen-binding fragments thereof bystandard protocols known in the art.

In other aspects of the invention, the FoxP3 molecules and theantibodies and other binding molecules, as described herein, can be usedfor the treatment or prevention of disorders. When “disorder” is usedherein, it refers to any pathological condition where the FoxP3polypeptides are aberrantly expressed. An example of such a disorder iscancer, particularly melanoma, bladder cancer, prostate cancer, breastcancer, colon cancer, lung cancer, glioblastoma and renal cellcarcinoma. In another aspect or the invention, such molecules can beused to inhibit immunological tolerance of tumors, by inhibiting themechanism by which FoxP3 contributes to tolerance.

Conventional treatment for cancer may include, but is not limited to:surgical intervention, chemotherapy, radiotherapy, and adjuvant systemictherapies. In one aspect of the invention, treatment may includeadministering binding polypeptides such as antibodies that specificallybind to the FoxP3 polypeptide. These binding polypeptides can beoptionally linked to one or more detectable markers, antitumor agents orimmunomodulators as described above.

Cancer treatment or prevention, in another aspect of the invention,includes administering antisense molecules or molecules that produce RNAinterference (RNAi) to reduce the expression level of FoxP3 nucleicacids or polypeptides and/or function level of FoxP3 polypeptides of theinvention in the subject in cancers where a FoxP3 molecule isup-regulated. The use of RNAi involves the use of double-stranded RNA(dsRNA) to block gene expression (see: Sui, G, et al, Proc Natl. Acad.Sci. U.S.A. 99:5515-5520, 2002). Methods of applying RNAi strategies inembodiments of the invention are known and understood by one of ordinaryskill in the art.

Methods in which small interfering RNA (siRNA) molecules are used toreduce the expression of FoxP3 may be used. In one aspect, a cell iscontacted with a siRNA molecule to produce RNA interference (RNAi) thatreduces expression of FoxP3. The siRNA molecule is directed againstnucleic acids coding for FoxP3 (e.g. RNA transcripts includinguntranslated and translated regions). In a preferred aspect of theinvention the siRNA is targeted to a FoxP3 splice variant in which exons1 and 4 are joined, e.g., splice variants including SEQ ID NO:6. Theexpression level of the targeted FoxP3 molecules can be determined usingwell known methods such as FACS or Western blotting for determining thelevel of protein expression and Northern blotting or RT-PCR fordetermining the level of mRNA transcript of the FoxP3 gene.

As used herein, a “siRNA molecule” is a double stranded RNA molecule(dsRNA) consisting of a sense and an antisense strand or a singlestranded molecule that has a dsRNA component, for example a section ofthe molecule that hybridizes to itself (e.g., a “hairpin” structure).The antisense strand of the siRNA molecule is a complement of the sensestrand (Tuschl, T. et al., 1999, Genes & Dev., 13:3191-3197; Elbashir,S. M. et al., 2001, EMBO J., 20:6877-6888; incorporated herein byreference). In one embodiment the last nucleotide at the 3′ end of theantisense strand may be any nucleotide and is not required to becomplementary to the region of the target gene. The siRNA molecule maybe 19-23 nucleotides in length and form a hairpin structure. In onepreferred embodiment the siRNA molecule includes a two nucleotide 3′overhang on the sense strand. In a second preferred embodiment the twonucleotide overhang is thymidine-thymidine (TT). The siRNA moleculecorresponds to at least a portion of the FoxP3 gene, preferably thenovel FoxP3 splice variant described herein. In one embodiment the siRNAmolecule corresponds to a region selected from a cDNA target genebeginning between 50 to 100 nucleotides downstream of the start codon.In a preferred embodiment the first nucleotide of the siRNA molecule isa purine.

The siRNA molecules can be plasmid-based. In a preferred method, a FoxP3nucleic acid sequence is amplified using the well known technique ofpolymerase chain reaction (PCR). The use of the entire polypeptideencoding sequence is not necessary; as is well known in the art, aportion of the polypeptide encoding sequence is sufficient for RNAinterference. The PCR fragment is inserted into a vector using routinetechniques well known to those of skill in the art. Combinations ofFoxP3 siRNA molecules can be expressed from a single vector or frommultiple vectors introduced into cells.

In one aspect of the invention a mammalian vector comprising FoxP3coding sequence is provided. The mammalian vectors include but are notlimited to the pSUPER RNAi vectors (Brummelkamp, T. R. et al., 2002,Science, 296:550-553, incorporated herein by reference). In oneembodiment a nucleotide coding sequence can be inserted into themammalian vector using restriction sites, creating a stem-loopstructure. In a second embodiment, the mammalian vector may comprise thepolymerase-III H1-RNA gene promoter. The polymerase-III H1-RNA promoterproduces a RNA transcript lacking a polyadenosine tail and has awell-defined start of transcription and a termination signal consistingof five thymidines (T5) in a row. The cleavage of the transcript at thetermination site occurs after the second uridine and yields a transcriptresembling the ends of synthetic siRNAs containing two 3′ overhanging Tor U nucleotides. The antisense strand of the siRNA molecule hybridizesto the corresponding region of the mRNA of the target gene.

Preferred systems for mRNA expression in mammalian cells are those suchas pSUPER RNAi system as described in Brummelkamp et al. (2002, Science,296:550-553). Other examples include but are not limited to pSUPER.neo,pSUPER.neo+gfp, pSUPER.puro, BLOCK-iT T7-TOPO linker,pcDNA1.2/V5-GW/lacZ, pENTR/U6, pLenti6-GW/U6-laminshrna, andpLenti6/BLOCK-iT-DEST. These vectors are available from suppliers suchas Invitrogen, and one of skill in the art would be able to obtain anduse them.

The invention includes kits for assaying the expression of FoxP3. Anexample of a kit may include an antibody or antigen-binding fragmentthereof, that binds specifically to a FoxP3 polypeptide. The antibody,or antigen-binding fragment thereof, may be applied to a tissue or cellsample from a patient with cancer or suspected of having cancer and thesample then processed to assess whether specific binding occurs betweenthe antibody and an antigen or other component of the sample. Inaddition, the antibody, or antigen-binding fragment thereof, may beapplied to a body fluid sample, such as serum, from a subject, eithersuspected of having cancer, diagnosed with cancer, or believed to befree of cancer. As will be understood by one of skill in the art, suchbinding assays may also be performed with a sample or object contactedwith an antibody and/or FoxP3 polypeptide that is in solution, forexample in a 96-well plate, or applied directly to a solid support(i.e., an object's surface).

Another example of a kit of the invention is a kit that providescomponents necessary to determine the level of expression of one or moreFoxP3 nucleic acid molecules of the invention. Such components mayinclude primers useful for amplification of one or more FoxP3 nucleicacid molecules and/or other chemicals for PCR amplification. Anotherexample of a kit of the invention is a kit that provides componentsnecessary to determine the level of expression of one or more FoxP3nucleic acid molecules of the invention using a method of hybridization.

The foregoing kits can include instructions or other printed material onhow to use the various components of the kits for diagnostic purposes.

The invention further includes nucleic acid or protein microarrays(including antibody arrays) for the analysis of expression of FoxP3polypeptides or nucleic acids encoding such antigens. In this aspect ofthe invention, standard techniques of microarray technology are utilizedto assess expression of the FoxP3 polypeptides and/or identifybiological constituents that bind such antigens. The constituents ofbiological samples include antibodies, lymphocytes (particularly Tlymphocytes), and the like. Microarray substrates include but are notlimited to glass, silica, aluminosilicates, borosilicates, metal oxidessuch as alumina and nickel oxide, various clays, nitrocellulose, ornylon. The microarray substrates may be coated with a compound toenhance synthesis of a probe (peptide or nucleic acid) on the substrate.Coupling agents or groups on the substrate can be used to covalentlylink the first nucleotide or amino acid to the substrate. A variety ofcoupling agents or groups are known to those of skill in the art.Peptide or nucleic acid probes thus can be synthesized directly on thesubstrate in a predetermined grid. Alternatively, peptide or nucleicacid probes can be spotted on the substrate, and in such cases thesubstrate may be coated with a compound to enhance binding of the probeto the substrate. In these embodiments, presynthesized probes areapplied to the substrate in a precise, predetermined volume and gridpattern, preferably utilizing a computer-controlled robot to apply probeto the substrate in a contact-printing manner or in a non-contact mannersuch as ink jet or piezo-electric delivery. Probes may be covalentlylinked to the substrate. Nucleic acid probes preferably are linked usingUV irradiation or heat.

Protein microarray technology, which is also known by other namesincluding protein chip technology and solid-phase protein arraytechnology, is well known to those of ordinary skill in the art and isbased on, but not limited to, obtaining an array of identified peptidesor proteins on a fixed substrate, binding target molecules or biologicalconstituents to the peptides, and evaluating such binding. See, e.g., G.MacBeath and S. L. Schreiber, “Printing Proteins as Microarrays forHigh-Throughput Function Determination,” Science 289(5485):1760-1763,2000.

Targets are peptides or proteins and may be natural or synthetic. Thetissue may be obtained from a subject or may be grown in culture (e.g.from a cell line).

In some embodiments of the invention, one or more control peptide orprotein molecules are attached to the substrate. Preferably, controlpeptide or protein molecules allow determination of factors such aspeptide or protein quality and binding characteristics, reagent qualityand effectiveness, hybridization success, and analysis thresholds andsuccess.

Nucleic acid arrays, particularly arrays that bind FoxP3 nucleic acidsequences, also can be used for diagnostic applications, such as foridentifying subjects that have a condition characterized by aberrantFoxP3 molecule expression, e.g., cancer. Nucleic acid microarraytechnology, which is also known by other names including: DNA chiptechnology, gene chip technology, and solid-phase nucleic acid arraytechnology, is well known to those of ordinary skill in the art and isbased on, but not limited to, obtaining an array of identified nucleicacid probes on a fixed substrate, labeling target molecules withreporter molecules (e.g., radioactive, chemiluminescent, or fluorescenttags such as fluorescein, Cye3-dUTP, or Cye5-dUTP), hybridizing targetnucleic acids to the probes, and evaluating target-probe hybridization.A probe with a nucleic acid sequence that perfectly matches the targetsequence will, in general, result in detection of a strongerreporter-molecule signal than will probes with less perfect matches.Many components and techniques utilized in nucleic acid microarraytechnology are presented in The Chipping Forecast, Nature Genetics, Vol.21, January 1999, the entire contents of which is incorporated byreference herein.

Targets for microarrays are nucleic acids selected from the group,including but not limited to: DNA, genomic DNA, cDNA, RNA, mRNA and maybe natural or synthetic. In all embodiments, nucleic acid targetmolecules from human tissue are preferred. The tissue may be obtainedfrom a subject or may be grown in culture (e.g. from a cell line).

In embodiments of the invention one or more control nucleic acidmolecules are attached to the substrate. Preferably, control nucleicacid molecules allow determination of factors such as nucleic acidquality and binding characteristics, reagent quality and effectiveness,hybridization success, and analysis thresholds and success. Controlnucleic acids may include but are not limited to expression products ofgenes such as housekeeping genes or fragments thereof.

According to a further aspect of the invention, compositions containingthe FoxP3 nucleic acid molecules, siRNA molecules, antisenseoligonucleotides, proteins, and binding polypeptides of the inventionare provided. The compositions contain any of the foregoing therapeuticagents in a carrier, optionally a pharmaceutically acceptable carrier.Thus, in a related aspect, the invention provides a method for forming amedicament that involves placing a therapeutically effective amount ofthe therapeutic agent in the pharmaceutically acceptable carrier to formone or more doses. The effectiveness of treatment or prevention methodsof the invention can be determined using standard diagnostic methodsdescribed herein.

When administered, the therapeutic compositions of the present inventionare administered in pharmaceutically acceptable preparations. Suchpreparations may routinely contain pharmaceutically acceptableconcentrations of salt, buffering agents, preservatives, compatiblecarriers, supplementary immune potentiating agents such as adjuvants andcytokines, and optionally other therapeutic agents.

As used herein, the term “pharmaceutically acceptable” means a non-toxicmaterial that does not interfere with the effectiveness of thebiological activity of the active ingredients. The term “physiologicallyacceptable” refers to a non-toxic material that is compatible with abiological system such as a cell, cell culture, tissue, or organism. Thecharacteristics of the carrier will depend on the route ofadministration. Physiologically and pharmaceutically acceptable carriersinclude diluents, fillers, salts, buffers, stabilizers, solubilizers,and other materials which are well known in the art. The term “carrier”denotes an organic or inorganic ingredient, natural or synthetic, withwhich the active ingredient is combined to facilitate the application.The components of the pharmaceutical compositions also are capable ofbeing co-mingled with the molecules of the present invention, and witheach other, in a manner such that there is no interaction which wouldsubstantially impair the desired pharmaceutical efficacy.

The therapeutics of the invention can be administered by anyconventional route, including injection or by gradual infusion overtime. The administration may, for example, be oral, intravenous,intratumoral, intraperitoneal, intramuscular, intracavity, subcutaneous,or transdermal. When antibodies are used therapeutically, a preferredroute of administration is by pulmonary aerosol. Techniques forpreparing aerosol delivery systems containing antibodies are well knownto those of skill in the art. Generally, such systems should utilizecomponents which will not significantly impair the biological propertiesof the antibodies, such as the paratope binding capacity (see, forexample, Sciarra and Cutie, “Aerosols,” in Remington's PharmaceuticalSciences, 18th edition, 1990, pp 1694-1712). Those of skill in the artcan readily determine the various parameters and conditions forproducing antibody aerosols without undue experimentation. When usingantisense preparations of the invention, slow intravenous administrationis preferred.

The compositions of the invention are administered in effective amounts.An “effective amount” is that amount of a FoxP3 nucleic acid composition(preferably siRNA or antisense oligonucleotides) that alone, or togetherwith further doses, produces the desired response, e.g., a reduction ofexpression of FoxP3 nucleic acids or polypeptide. In the case oftreating a particular disease or condition characterized by expressionof one or more FoxP3 polypeptides, such as cancer, the desired responseis inhibiting the progression of the disease. This may involve onlyslowing the progression of the disease temporarily, although morepreferably, it involves halting the progression of the diseasepermanently. This can be monitored by routine methods or can bemonitored according to diagnostic methods of the invention discussedherein. The desired response to treatment of the disease or conditionalso can be delaying the onset or even preventing the onset of thedisease or condition.

Such amounts will depend, of course, on the particular condition beingtreated, the severity of the condition, the individual patientparameters including age, physical condition, size and weight, theduration of the treatment, the nature of concurrent therapy (if any),the specific route of administration and like factors within theknowledge and expertise of the health practitioner. These factors arewell known to those of ordinary skill in the art and can be addressedwith no more than routine experimentation. It is generally preferredthat a maximum dose of the individual components or combinations thereofbe used, that is, the highest safe dose according to sound medicaljudgment. It will be understood by those of ordinary skill in the art,however, that a patient may insist upon a lower dose or tolerable dosefor medical reasons, psychological reasons or for virtually any otherreasons.

The pharmaceutical compositions used in the foregoing methods preferablyare sterile and contain an effective amount of FoxP3 nucleic acid (e.g.,siRNA or antisense oligonucleotide) for producing the desired responsein a unit of weight or volume suitable for administration to a patient.The response can, for example, be measured by determining FoxP3expression following administration of the FoxP3 composition bymeasuring the expression of FoxP3, or by observing the physiologicaleffects of the FoxP3 composition, such as regression of a tumor ordecrease of disease symptoms. Other assays will be known to one ofordinary skill in the art and can be employed for measuring the level ofthe response.

The present invention therefore provides pharmaceutical compositionscomprising an agent that reduces FoxP3 nucleic acid or polypeptideexpression. These pharmaceutical compositions may be administeredorally, rectally, parenterally, intratumorally, intrathecally,intracistemally, intravaginally, intraperitoneally, topically (as bypowders, ointments, drops or transdermal patch), bucally, or as an oralor nasal spray. As used herein, “pharmaceutically acceptable carrier” isintended to mean a non-toxic solid, semisolid or liquid filler, diluent,encapsulating material or formulation auxiliary of any type. The term“parenteral” as used herein refers to modes of administration whichinclude intravenous, intramuscular, intrathecal, intraperitoneal,infrasternal, subcutaneous and intraarticular injection and infusion.

When antibodies are used therapeutically, a preferred route ofadministration is by pulmonary aerosol. Techniques for preparing aerosoldelivery systems containing antibodies are well known to those of skillin the art. Generally, such systems should utilize components which willnot significantly impair the biological properties of the antibodies,such as the paratope binding capacity (see, for example, Sciarra andCutie, “Aerosols,” in Remington's Pharmaceutical Sciences, 18th edition,1990, pp 1694-1712). Those of skill in the art can readily determine thevarious parameters and conditions for producing antibody aerosolswithout undue experimentation.

Where FoxP3 polypeptides are used for vaccination, modes ofadministration which effectively deliver the FoxP3 polypeptide andadjuvant, such that an immune response to the polypeptide is increased,can be used. For administration of a FoxP3 polypeptide in adjuvant,preferred methods include intradermal, intravenous, intramuscular andsubcutaneous administration. Although these are preferred embodiments,the invention is not limited by the particular modes of administrationdisclosed herein. Standard references in the art (e.g., Remington'sPharmaceutical Sciences, 18th edition, 1990) provide modes ofadministration and formulations for delivery of immunogens with adjuvantor in a non-adjuvant carrier.

One of ordinary skill will recognize that the choice of a particularmode of administration can be made empirically based upon considerationssuch as the particular disease state being treated; the type and degreeof the response to be achieved; the specific agent or compositionemployed; the age, body weight, general health, sex and diet of thepatient; the time of administration and rate of excretion of the agentor composition; the duration of the treatment; drugs (such as achemotherapeutic agent or other cancer therapeutic) used in combinationor coincidental with the specific composition; and like factors wellknown in the medical arts.

Pharmaceutical compositions of the present invention for parenteralinjection may comprise pharmaceutically acceptable sterile aqueous ornonaqueous solutions, dispersions, suspensions or emulsions as well assterile powders for reconstitution into sterile injectable solutions ordispersions just prior to use. Illustrative examples of suitable aqueousand nonaqueous carriers, diluents, solvents or vehicles include, but arenot limited to, water, ethanol, polyols (such as glycerol, propyleneglycol, polyethylene glycol, and the like), carboxymethylcellulose andsuitable mixtures thereof, vegetable oils (such as olive oil), andinjectable organic esters such as ethyl oleate. Proper fluidity can bemaintained, for example, by the use of coating materials such aslecithin, by the maintenance of the required particle size in the caseof dispersions, and by the use of surfactants.

As used herein, the term “pharmaceutically acceptable” means a non-toxicmaterial that does not interfere with the effectiveness of thebiological activity of the active ingredients. The term “physiologicallyacceptable” refers to a non-toxic material that is compatible with abiological system such as a cell, cell culture, tissue, or organism. Thecharacteristics of the carrier will depend on the route ofadministration. Physiologically and pharmaceutically acceptable carriersinclude diluents, fillers, salts, buffers, stabilizers, solubilizers,and other materials which are well known in the art. The term “carrier”denotes an organic or inorganic ingredient, natural or synthetic, withwhich the active ingredient is combined to facilitate the application.The components of the pharmaceutical compositions also are capable ofbeing co-mingled with the molecules of the present invention, and witheach other, in a manner such that there is no interaction which wouldsubstantially impair the desired pharmaceutical efficacy.

The compositions of the present invention may also contain adjuvantssuch as preservatives, wetting agents, emulsifying agents, anddispersing agents. Prevention of the action of microorganisms may beensured by the inclusion of various antibacterial and antifungal agents,for example, parabens, chlorobutanol, phenol sorbic acid, and the like.It may also be desirable to include isotonic agents such as sugars,sodium chloride, and the like. Prolonged absorption of the injectablepharmaceutical form may be brought about by the inclusion of agentswhich delay absorption such as aluminum monostearate and gelatin.

In some cases, in order to prolong the effect of the therapeutic agentor inhibitor, it is desirable to slow the absorption from subcutaneousor intramuscular injection. This may be accomplished by the use of aliquid suspension of crystalline or amorphous material with poor watersolubility. The rate of absorption of the drug then depends upon itsrate of dissolution which, in turn, may depend upon crystal size andcrystalline form. Alternatively, delayed absorption of a parenterallyadministered drug form is accomplished by dissolving or suspending thedrug in an oil vehicle.

Injectable depot forms are made by forming microencapsule matrices ofthe drug in biodegradable polymers such as polylactide-polyglycolide.Depending upon the ratio of drug to polymer and the nature of theparticular polymer employed, the rate of drug release can be controlled.Examples of other biodegradable polymers include poly(orthoesters) andpoly(anhydrides). Depot injectable formulations are also prepared byentrapping the drug in liposomes or microemulsions which are compatiblewith body tissues.

The injectable formulations can be sterilized, for example, byfiltration through a bacteria-retaining filter, or by incorporatingsterilizing agents in the form of sterile solid compositions which canbe dissolved or dispersed in sterile water or other sterile injectablemedium just prior to use.

Solid dosage forms for oral administration include, but are not limitedto, capsules, tablets, pills, powders, and granules. In such soliddosage forms, the active compounds are preferably mixed with at leastone pharmaceutically acceptable excipient or carrier such as sodiumcitrate or dicalcium phosphate and/or a) fillers or extenders such asstarches, lactose, sucrose, glucose, mannitol, and silicic acid, b)binders such as, for example, carboxymethylcellulose, alginates,gelatin, polyvinylpyrrolidone, sucrose, and acacia, c) humectants suchas glycerol, d) disintegrating agents such as agar-agar, calciumcarbonate, potato or tapioca starch, alginic acid, certain silicates,and sodium carbonate, e) solution retarding agents such as paraffin, f)absorption accelerators such as quaternary ammonium compounds, g)wetting agents such as, for example, cetyl alcohol and glycerolmonostearate, h) absorbents such as kaolin and bentonite clay, and i)lubricants such as talc, calcium stearate, magnesium stearate, solidpolyethylene glycols, sodium lauryl sulfate, and mixtures thereof. Inthe case of capsules, tablets and pills, the dosage form may alsocomprise buffering agents as appropriate.

Solid compositions of a similar type may also be employed as fillers insoft and hard filled gelatin capsules using such excipients as lactoseor milk sugar as well as high molecular weight polyethylene glycols andthe like.

The solid dosage forms of tablets, dragees, capsules, pills, andgranules can be prepared with coatings and shells such as entericcoatings and other coatings well known in the pharmaceutical formulatingart. They may optionally contain opacifying agents and can also be of acomposition that they release the active ingredient(s) only, orpreferentially, in a certain part of the intestinal tract, optionally,in a delayed manner. Illustrative examples of embedding compositionswhich can be used include polymeric substances and waxes.

Liquid dosage forms for oral administration include, but are not limitedto, pharmaceutically acceptable emulsions, solutions, suspensions,syrups and elixirs. In addition to the active compounds, the liquiddosage forms may contain inert diluents commonly used in the art suchas, for example, water or other solvents, solubilizing agents andemulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate,ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol,1,3-butylene glycol, dimethyl formamide, oils (in particular,cottonseed, groundnut, corn, germ, olive, castor, and sesame oils),glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fattyacid esters of sorbitan, and mixtures thereof.

Besides inert diluents, the oral compositions may also contain adjuvantssuch as wetting agents, emulsifying and suspending agents, sweetening,flavoring, and perfuming agents.

Suspensions, in addition to the active compounds, may contain suspendingagents as, for example, ethoxylated isostearyl alcohols, polyoxyethylenesorbitol and sorbitan esters, microcrystalline cellulose, aluminummetahydroxide, bentonite, agar-agar, and tragacanth, and mixturesthereof.

The agent or inhibitor can also be administered in the form ofliposomes. As is known to those skilled in the art, liposomes aregenerally derived from phospholipids or other lipid substances.Liposomes are formed by mono- or multi-lamellar hydrated liquid crystalsthat are dispersed in an aqueous medium. Any non-toxic, physiologicallyacceptable and metabolizable lipid capable of forming liposomes can beused. The present compositions in liposome form can contain, in additionto the agent or inhibitor, stabilizers, preservatives, excipients, andthe like. Preferred lipids are phospholipids and phosphatidyl cholines(lecithins), both natural and synthetic. Methods to form liposomes areknown in the art. See, e.g., Prescott, ed., METHODS IN CELL BIOLOGY,Volume XIV, Academic Press, New York, N.Y. (1976), p. 33 et seq.

The agents of the present invention can be formulated according to knownmethods to prepare pharmaceutically acceptable compositions, wherebythese materials, or their functional derivatives, are combined in amixture with a pharmaceutically acceptable carrier vehicle. Suitablevehicles and their formulation, inclusive of other human proteins, e.g.,human serum albumin, are well known in the art. In order to form apharmaceutically acceptable composition suitable for effectiveadministration, such compositions will contain an effective amount ofone or more agents of the present invention.

Additional pharmaceutical methods may be employed to control theduration of action. Controlled release preparations may be achievedthrough the use of polymers to complex or absorb the therapeutic agentsof the invention. The controlled delivery may be exercised by selectingappropriate macromolecules (such as polyesters, polyamino acids,polyvinyl, pyrrolidone, ethylenevinylacetate, methylcellulose,carboxymethylcellulose, or protamine sulfate) and methods ofincorporation in order to control release. Another possible method tocontrol the duration of action by controlled release preparations is toincorporate antibodies into particles of a polymeric material such aspolyesters, polyamino acids, hydrogels, poly(lactic acid) or ethylenevinyl acetate copolymers. Alternatively, instead of incorporating theseagents into polymeric particles, it is possible to entrap thesematerials in microcapsules prepared, for example, by coacervationtechniques or by interfacial polymerization, for example,hydroxymethylcellulose or gelatine-microcapsules andpoly(methylmethacylate) microcapsules, respectively, or in colloidaldrug delivery systems, for example, liposomes, albumin microspheres,microemulsions, nanoparticles, and nanocapsules or in macroemulsions.

The pharmaceutical formulations of the present invention are prepared,for example, by admixing the active agent with solvents and/or carriers,optionally using emulsifiers and/or dispersants, while if water is usedas the diluent, organic solvents may be used as solubilizing agents orauxiliary solvents. As described above, the excipients used include, forexample, water, pharmaceutically acceptable organic solvents such asparaffins, vegetable oils, mono- or polyfunctional alcohols, carrierssuch as natural mineral powders, synthetic mineral powders, sugars,emulsifiers and lubricants.

One of ordinary skill will appreciate that effective amounts of theinventive therapeutic agents can be determined empirically and may beemployed in pure form or, where such forms exist, in pharmaceuticallyacceptable salt, ester or prodrug form. The agonist or antagonist my beadministered in compositions in combination with one or morepharmaceutically acceptable excipients. It will be understood that, whenadministered to a human patient, the total daily usage of the agents andcompositions of the present invention will be decided by the attendingphysician within the scope of sound medical judgement. The specifictherapeutically effective dose level for any particular patient willdepend upon a variety of factors including the type and degree of theresponse to be achieved; the specific agent or composition employed; theage, body weight, general health, sex and diet of the patient; the timeof administration, route of administration, and rate of excretion of theagent or composition; the duration of the treatment; drugs (such as achemotherapeutic agent) used in combination or coincidental with thespecific composition; and like factors well known in the medical arts.

Techniques of dosage determination are well known in the art forantibody and peptide agents. In general, it is desirable to provide apatient with a dosage of antibody or peptide agent in the range of fromabout 1 pg/kg to 10 mg/kg (body weight of patient). The therapeuticallyeffective dose can be lowered if the agent of the present invention isadditionally administered with another compound. As used herein, onecompound is said to be additionally administered with a second compoundwhen the administration of the two compounds is in such proximity oftime that both compounds can be detected at the same time in thepatient's serum.

For example, satisfactory results are obtained by oral administration oftherapeutic dosages on the order of from 0.05 to 10 mg/kg/day,preferably 0.1 to 7.5 mg/kg/day, more preferably 0.1 to 2 mg/kg/day,administered once or, in divided doses, 2 to 4 times per day. Onadministration parenterally, for example by i.v. drip or infusion,dosages on the order of from 0.01 to 5 mg/kg/day, preferably 0.05 to 1.0mg/kg/day and more preferably 0.1 to 1.0 mg/kg/day can be used. Suitabledaily dosages for patients are thus on the order of from 2.5 to 500 mgp.o., preferably 5 to 250 mg p.o., more preferably 5 to 100 mg p.o., oron the order of from 0.5 to 250 mg i.v., preferably 2.5 to 125 mg i.v.and more preferably 2.5 to 50 mg i.v.

Dosaging may also be arranged in a patient specific manner to provide apredetermined concentration of an agent in the blood. Thus patientdosaging may be adjusted to achieve regular on-going trough bloodlevels, on the order of from 50 to 1000 ng/ml, preferably 150 to 500ng/ml.

The agents of the present invention are intended to be provided to apatient in an amount sufficient to reduce the amount of expression ofFoxP3 nucleic acid and/or polypeptide, i.e., an effective amount. Anamount is said to be sufficient to “reduce the amount of expression ofFoxP3 nucleic acid and/or polypeptide” if the dosage, route ofadministration, etc. of the agent is sufficient to reduce the amount ofexpression of FoxP3 nucleic acid and/or polypeptide as detected by anymethodology known to persons skilled in the art, particularly thosedescribed herein.

In the case of treating a particular cancer, the desired response isinhibiting the progression of the cancer. This may involve only slowingthe progression of the cancer temporarily, although more preferably, itinvolves halting the progression of the cancer permanently. This can bemonitored by routine methods or can be monitored according to diagnosticmethods of the invention discussed herein. The desired response totreatment of the disease or condition also can be delaying the onset oreven preventing the onset of the disease or condition. Such an effectcan be assayed, for example, by examining the onset of cancer symptomsoccurring in vivo, determining proliferation or tumorigenicity of cancercells (e.g., in animal tumor explant models), or by correlating in vitroblocking studies with predicted in vivo efficacy.

The agents that reduce the amount of expression of FoxP3 nucleic acidand/or polypeptide can be administered in combination with a vaccinetargeted against FoxP3 and/or cancer-testis (CT) antigens, which arewell know to the person skilled in the art. Thus the invention involvesthe use of various materials disclosed herein to “immunize” subjects oras “vaccines”. As used herein, “immunization” or “vaccination” meansincreasing or activating an immune response against an antigen. It doesnot require elimination or eradication of a condition but rathercontemplates the clinically favorable enhancement of an immune responsetoward an antigen.

Generally accepted animal models can be used for testing of immunizationagainst cancer using one or more CT antigens. For example, human cancercells can be introduced into a mouse to create a tumor, and FoxP3 andone or more CT antigens, such as NY-ESO-1, or nucleic acids encodingthese can be delivered by the methods described herein. The effect onthe cancer cells (e.g., reduction of tumor size) can be assessed as ameasure of the effectiveness of the combination therapy. Of course,testing of the foregoing animal model using more conventional methodsfor immunization can include the administration of one or more CTantigen polypeptides or fragments derived therefrom, optionally combinedwith one or more adjuvants and/or cytokines to boost the immuneresponse.

Methods for immunization, including formulation of a vaccine compositionand selection of doses, route of administration and the schedule ofadministration (e.g. primary and one or more booster doses), are wellknown in the art.

As part of the immunization compositions, one or more antigens orimmunogenic fragments thereof are administered with one or moreadjuvants to induce an immune response or to increase an immuneresponse. An adjuvant is a substance incorporated into or administeredwith antigen which potentiates the immune response. Adjuvants mayenhance the immunological response by providing a reservoir of antigen(extracellularly or within macrophages), activating macrophages andstimulating specific sets of lymphocytes. Adjuvants of many kinds arewell known in the art. Specific examples of adjuvants includemonophosphoryl lipid A (MPL, SmithKline Beecham), a congener obtainedafter purification and acid hydrolysis of Salmonella minnesota Re 595lipopolysaccharide; saponins including QS21 (SmithKline Beecham), a pureQA-21 saponin purified from Quillja saponaria extract; DQS21, describedin PCT application WO96/33739 (SmithKline Beecham), ISCOMATRIX® (CSLLtd., Parkville, Victoria, Australia) derived from the bark of theQuillaia saponaria molina tree; QS-7, QS-17, QS-18, and QS-L1 (So etal., Mol. Cells. 7:178-186, 1997); incomplete Freund's adjuvant;complete Freund's adjuvant; montanide; alum; CpG oligonucleotides (seee.g. Kreig et al., Nature 374:546-9, 1995; U.S. Pat. No. 6,207,646) andother immunostimulatory oligonucleotides; various water-in-oil emulsionsprepared from biodegradable oils such as squalene and/or tocopherol; andfactors that are taken up by the so-called ‘toll-like receptor 7’ oncertain immune cells that are found in the outside part of the skin,such as imiquimod (3M, St. Paul, Minn.). Preferably, the antigens areadministered mixed with a combination of DQS21/MPL or ISCOMATRIX®. Theratio of DQS21 to MPL typically will be about 1:10 to 10:1, preferablyabout 1:5 to 5:1 and more preferably about 1:1. Typically for humanadministration, DQS21 and MPL will be present in a vaccine formulationin the range of about 1 μg to about 100 μg. Other adjuvants are known inthe art and can be used in the invention (see, e.g. Goding, MonoclonalAntibodies: Principles and Practice, 2nd Ed., 1986). Methods for thepreparation of mixtures or emulsions of polypeptide and adjuvant arewell known to those of skill in the art of vaccination.

Other agents which stimulate the immune response of the subject can alsobe administered to the subject. For example, other cytokines are alsouseful in vaccination protocols as a result of their lymphocyteregulatory properties. Many other cytokines useful for such purposeswill be known to one of ordinary skill in the art, includinginterleukin-12 (IL-12) which has been shown to enhance the protectiveeffects of vaccines (see, e.g., Science 268: 1432-1434, 1995), GM-CSF,IL-18 and IL-15 (Klebanoff et al. Proc. Natl. Acad. Sci. USA 2004101:1969-74). Thus cytokines can be administered in conjunction withantigens and adjuvants to increase the immune response to the antigens.

There are a number of immune response potentiating compounds that can beused in vaccination protocols. These include costimulatory moleculesprovided in either protein or nucleic acid form. Such costimulatorymolecules include the B7-1 and B7-2 (CD80 and CD86 respectively)molecules which are expressed on dendritic cells (DC) and interact withthe CD28 molecule expressed on the T cell. This interaction providescostimulation (signal 2) to an antigen/MHC/TCR stimulated (signal 1) Tcell, increasing T cell proliferation and effector function. B7 alsointeracts with CTLA4 (CD152) on T cells and studies involving CTLA4 andB7 ligands indicate that the B7-CTLA4 interaction can enhance antitumorimmunity and CTL proliferation (Zheng P., et al. Proc. Natl. Acad. Sci.USA 95 (11):6284-6289 (1998)).

B7 typically is not expressed on tumor cells so they are not efficientantigen presenting cells (APCs) for T cells. Induction of B7 expressionwould enable the tumor cells to stimulate more efficiently CTLproliferation and effector function. A combination of B7/IL-6/IL-12costimulation has been shown to induce IFN-gamma and a Th1 cytokineprofile in the T cell population leading to further enhanced T cellactivity (Gajewski et al., J. Immunol, 154:5637-5648 (1995)). Tumor celltransfection with B7 has been discussed in relation to in vitro CTLexpansion for adoptive transfer immunotherapy by Wang et al., (J.Immunol., 19:1-8 (1986)). Other delivery mechanisms for the B7 moleculeinclude nucleic acid (naked DNA) immunization (Kim J., et al. Nat.Biotechnol., 15:7:641-646 (1997)) and recombinant viruses such as adenoand pox (Wendtner et al., Gene Ther., 4:7:726-735 (1997)). These systemsare all amenable to the construction and use of expression cassettes forthe coexpression of B7 with other molecules of choice such as theantigens or fragment(s) of antigens discussed herein (includingpolytopes) or cytokines. These delivery systems can be used forinduction of the appropriate molecules in vitro and for in vivovaccination situations. The use of anti-CD28 antibodies to directlystimulate T cells in vitro and in vivo could also be considered.Similarly, the inducible co-stimulatory molecule ICOS which induces Tcell responses to foreign antigen could be modulated, for example, byuse of anti-ICOS antibodies (Hutloff et al., Nature 397:263-266, 1999).

Lymphocyte function associated antigen-3 (LFA-3) is expressed on APCsand some tumor cells and interacts with CD2 expressed on T cells. Thisinteraction induces T cell IL-2 and IFN-gamma production and can thuscomplement but not substitute, the B7/CD28 costimulatory interaction(Parra et al., J. Immunol., 158:637-642 (1997), Fenton et al., J.Immunother., 21:2:95-108 (1998)).

Lymphocyte function associated antigen-1 (LFA-1) is expressed onleukocytes and interacts with ICAM-1 expressed on APCs and some tumorcells. This interaction induces T cell IL-2 and IFN-gamma production andcan thus complement but not substitute, the B7/CD28 costimulatoryinteraction (Fenton et al., J. Immunother., 21:2:95-108 (1998)). LFA-1is thus a further example of a costimulatory molecule that could beprovided in a vaccination protocol in the various ways discussed abovefor B7.

Complete CTL activation and effector function requires Th cell helpthrough the interaction between the Th cell CD40L (CD40 ligand) moleculeand the CD40 molecule expressed by DCs (Ridge et al., Nature, 393:474(1998), Bennett et al., Nature, 393:478 (1998), Schoenberger et al.,Nature, 393:480 (1998)). This mechanism of this costimulatory signal islikely to involve upregulation of B7 and associated IL-6/IL-12production by the DC (APC). The CD40-CD40L interaction thus complementsthe signal 1 (antigen/MHC-TCR) and signal 2 (B7-CD28) interactions.

The use of anti-CD40 antibodies to stimulate DC cells directly, would beexpected to enhance a response to tumor antigens which are normallyencountered outside of an inflammatory context or are presented bynon-professional APCs (tumor cells). In these situations Th help and B7costimulation signals are not provided.

The invention contemplates delivery of nucleic acids, polypeptides orfragments thereof for vaccination. Delivery of polypeptides andfragments thereof can be accomplished according to standard vaccinationprotocols which are well known in the art. In another embodiment, thedelivery of nucleic acid is accomplished by ex vivo methods, i.e. byremoving a cell from a subject, genetically engineering the cell toinclude one or more CT antigens, and reintroducing the engineered cellinto the subject. One example of such a procedure is outlined in U.S.Pat. No. 5,399,346 and in exhibits submitted in the file history of thatpatent, all of which are publicly available documents. In general, itinvolves introduction in vitro of a functional copy of a gene into acell(s) of a subject, and returning the genetically engineered cell(s)to the subject. The functional copy of the gene is under operablecontrol of regulatory elements which permit expression of the gene inthe genetically engineered cell(s). Numerous transfection andtransduction techniques as well as appropriate expression vectors arewell known to those of ordinary skill in the art, some of which aredescribed in PCT application WO95/00654. In vivo nucleic acid deliveryusing vectors such as viruses and targeted liposomes also iscontemplated according to the invention.

A virus vector for delivering a nucleic acid encoding one or more CTantigens is selected from the group consisting of adenoviruses,adeno-associated viruses, poxviruses including vaccinia viruses andattenuated poxviruses, Semliki Forest virus, Venezuelan equineencephalitis virus, retroviruses, Sindbis virus, and Ty virus-likeparticle. Examples of viruses and virus-like particles which have beenused to deliver exogenous nucleic acids include: replication-defectiveadenoviruses (e.g., Xiang et al., Virology 219:220-227, 1996; Eloit etal., J. Virol. 7:5375-5381, 1997; Chengalvala et al., Vaccine15:335-339, 1997), a modified retrovirus (Townsend et al., J. Virol.71:3365-3374, 1997), a nonreplicating retrovirus (Irwin et al., J.Virol. 68:5036-5044, 1994), a replication defective Semliki Forest virus(Zhao et al., Proc. Natl. Acad. Sci. USA 92:3009-3013, 1995), canarypoxvirus and highly attenuated vaccinia virus derivative (Paoletti, Proc.Natl. Acad. Sci. USA 93:11349-11353, 1996), non-replicative vacciniavirus (Moss, Proc. Natl. Acad. Sci. USA 93:11341-11348, 1996),replicative vaccinia virus (Moss, Dev. Biol. Stand. 82:55-63, 1994),Venzuelan equine encephalitis virus (Davis et al., J. Virol.70:3781-3787, 1996), Sindbis virus (Pugachev et al., Virology212:587-594, 1995), and Ty virus-like particle (Allsopp et al., Eur. J.Immunol. 26:1951-1959, 1996). A preferred virus vector is an adenovirus.

Preferably the foregoing nucleic acid delivery vectors: (1) containexogenous genetic material that can be transcribed and translated in amammalian cell and that can induce an immune response in a host, and (2)contain on a surface a ligand that selectively binds to a receptor onthe surface of a target cell, such as a mammalian cell, and therebygains entry to the target cell.

Various techniques may be employed for introducing nucleic acids intocells, depending on whether the nucleic acids are introduced in vitro orin vivo in a host. Such techniques include transfection of nucleicacid-CaPO₄ precipitates, transfection of nucleic acids associated withDEAE, transfection or infection with the foregoing viruses including thenucleic acid of interest, liposome mediated transfection, and the like.For certain uses, it is preferred to target the nucleic acid toparticular cells. In such instances, a vehicle used for delivering anucleic acid into a cell (e.g., a retrovirus, or other virus; aliposome) can have a targeting molecule attached thereto. For example, amolecule such as an antibody specific for a surface membrane protein onthe target cell or a ligand for a receptor on the target cell can bebound to or incorporated within the nucleic acid delivery vehicle.Preferred antibodies include antibodies which selectively bind acancer-testis antigen, alone or as a complex with a MHC molecule.Especially preferred are monoclonal antibodies. Where liposomes areemployed to deliver the nucleic acids, proteins which bind to a surfacemembrane protein associated with endocytosis may be incorporated intothe liposome formulation for targeting and/or to facilitate uptake. Suchproteins include capsid proteins or fragments thereof tropic for aparticular cell type, antibodies for proteins which undergointernalization in cycling, proteins that target intracellularlocalization and enhance intracellular half life, and the like.Polymeric delivery systems also have been used successfully to delivernucleic acids into cells, as is known by those skilled in the art. Suchsystems even permit oral delivery of nucleic acids.

The administration of the agents of the present invention may be foreither prophylactic or therapeutic purpose. When providedprophylactically, the agent is provided in advance of any cancersymptoms. The prophylactic administration of the agent serves to preventor reduce the rate of onset of symptoms. When provided therapeutically,the agent is provided at (or after) the onset of the appearance ofsymptoms of actual disease. The therapeutic administration of the agentserves to reduce the severity and duration of cancer.

As described herein, reducing expression of FoxP3 nucleic acid and/orpolypeptide can be used for treatment of cancer. For human cancers,particular examples include, biliary tract cancer; bladder cancer;breast cancer; brain cancer including glioblastomas andmedulloblastomas; cervical cancer; choriocarcinoma; colon cancerincluding colorectal carcinomas; endometrial cancer; esophageal cancer;gastric cancer; head and neck cancer; hematological neoplasms includingacute lymphocytic and myelogenous leukemia, multiple myeloma,AIDS-associated leukemias and adult T-cell leukemia lymphoma;intraepithelial neoplasms including Bowen's disease and Paget's disease;liver cancer; lung cancer including small cell lung cancer and non-smallcell lung cancer; lymphomas including Hodgkin's disease and lymphocyticlymphomas; neuroblastomas; oral cancer including squamous cellcarcinoma; osteosarcomas; ovarian cancer including those arising fromepithelial cells, stromal cells, germ cells and mesenchymal cells;pancreatic cancer; prostate cancer; rectal cancer; sarcomas includingleiomyosarcoma, rhabdomyosarcoma, liposarcoma, fibrosarcoma, synovialsarcoma, neurosarcoma, chondrosarcoma, Ewing sarcoma, malignant fibroushistocytoma, glioma, esophageal cancer, hepatoma and osteosarcoma; skincancer including melanomas, Kaposi's sarcoma, basocellular cancer, andsquamous cell cancer; testicular cancer including germinal tumors suchas seminoma, non-seminoma (teratomas, choriocarcinomas), stromal tumors,and germ cell tumors; testicular cancer; thyroid cancer includingthyroid adenocarcinoma and medullar carcinoma; transitional cancer andrenal cancer including adenocarcinoma and Wilms tumor.

The treatments described herein can be combined with conventional cancertreatments. Conventional treatment for cancer may include, but is notlimited to: surgical intervention, chemotherapy, radiotherapy, andadjuvant systemic therapies. In one aspect of the invention, treatmentmay include administering binding polypeptides such as antibodies thatspecifically bind to the one or more CT antigens. These bindingpolypeptides can be optionally linked to one or more detectable markers,antitumor agents or immunomodulators as described herein and/or known inthe art.

The pharmaceutical agents of the invention may be administered alone, incombination with each other, and/or in combination with otheranti-cancer drug therapies and/or treatments. These therapies and/ortreatments may include, but are not limited to: surgical intervention,chemotherapy, radiotherapy, and adjuvant systemic therapies.

The invention also provides a pharmaceutical kit comprising one or morecontainers comprising one or more of the pharmaceutical compounds oragents of the invention. Additional materials may be included in any orall kits of the invention, and such materials may include, but are notlimited to buffers, water, enzymes, tubes, control molecules, etc. Thekit may also include instructions for the use of the one or morepharmaceutical compounds or agents of the invention for the treatment ofcancer.

The present invention is described in further detail in the followingnon-limiting examples.

EXAMPLES Materials and Methods

Cells, Tissue and Media

Complete medium (RF-10) consisted of RPMI supplemented with 2 mMGlutamax, 100 U/ml penicillin, 100 μg/ml streptomycin and 10 mM HEPES(all from Invitrogen, Carlsbad, Calif.) and 10% FCS (fetal calf serum,Thermo Trace, Melbourne, VIC, Australia). Tumor cell lines and primaryfibroblast cultures (derived from normal human dermis or foreskintissue) were maintained in RF-10 and passaged when required usingtrypsin/EDTA (Invitrogen) or 2 mM EDTA in PBS, pH 7.4. Normal epidermalmelanocyte cultures were obtained from Lonza Biosciences (Basel,Switzerland).

Melanoma tissue collected following surgical resection wasformalin-fixed and embedded in paraffin for immunohistochemistry, orused to generate single cell suspensions as follows: tissue was finelychopped using a scalpel, gently homogenized to generate a single cellsuspension and remaining fragments and clumps of cells removed byfiltering. The cells were resuspended in FCS containing 10% DMSO(Sigma-Aldrich, Castle Hill, NSW, Australia) and cryopreserved in liquidnitrogen until required. The collection of tissue for these studies wasapproved by the Human Research and Ethics Committee (Austin Health,Melbourne, Australia), and all patients gave informed consent.

Peripheral blood mononuclear cells (PBMC) from buffy coats of healthydonors (Red Cross Blood Bank, Melbourne, Australia) were prepared byFicoll-Paque density gradient centrifugation (Amersham Biosciences,Uppsala, Sweden). NK cells, monocytes and CD4⁺ T cells were purifiedusing the NK Cell isolation kit or CD14 or CD4 Microbeads, respectively,according to the manufacturer's recommendations (Miltenyi Biotec,Bergisch Gladbach, Germany). Cell purity was greater than 96% asdetermined by flow cytometry. Monocyte-derived dendritic cells (moDC)were generated by plating monocytes at 5×10⁵ cells/ml in RF-10supplemented with GM-CSF plus IL-4 for 6-7 days. The Treg cell line wasgenerated following purification of CD25^(hi) T cells from adisaggregated tumor sample using CD3 microbeads (Miltenyi) followed byCD25 Dynabeads (Invitrogen). The cells were expanded using 1 μg/ml PHAand feeder cells in RF-10 containing 150 IU/ml IL-2.

Immunohistochemistry

Immunohistochemistry was performed on formalin-fixed paraffin sectionsafter EDTA buffer pH 8.0 (NeoMarkers, Fremont, Calif.) retrieval, asdescribed (41). All sections were incubated with 3% H₂O₂/PBS for 10minutes to block endogenous peroxidase. Rabbit polyclonal anti-FoxP3antibody (Abeam, Cambridge, UK) was used at a 1:500 dilution for 1 hour.Dako Envision+™ polymer (DakoCytomation, Carpinteria, Calif.) was usedas the secondary reagent and 3-amino-9-ethyl-carbazole (Sigma-Aldrich,St. Louis, Mo.) was used as the chromogen. All incubations wereperformed at room temperature using the Shandon Sequenza® immunostainer(Thermo Scientific, Waltham, Mass.). Slides were counterstained withMayer's haematoxylin (Amber Scientific, Belmont, Wash.). Application ofCrystalMount (Biomeda Corp., CA) preceded dehydration and mounting inDePeX (BDH 36125). Tonsil was used as a positive control for each runand a rabbit IgG (Vecta Laboratories, Burlingame, USA) negative controlwas included with every immunohistochemical test. Monoclonal antibody toMelan-A (clone A103) was produced at the Biological Production Facility,Ludwig Institute of Cancer Research.

Flow Cytometry and Cell Sorting

Fluorochrome-conjugated antibodies to human CD4 (clone UCHT2), CD19(clone HIB19), CD31 (clone WM59), CD90 (clone 5E10) and isotype-matchedcontrol antibodies were from BD Biosciences (Franklin Lakes, N.J.).Anti-CD3 (clone S4.1) was from Invitrogen, anti-MCSP (clone EP-1) wasfrom Miltenyi and anti-FoxP3 (clone 236A/E7) was from eBioscience (SanDiego, Calif.). Staining of surface antigens was performed in 96-wellplates by incubating the cells with an appropriate concentration ofantibody (as determined by titration) in FACS buffer (PBS+2% FCS+0.04%sodium azide) for 15 minutes at 4° C. FoxP3 staining was performed afterstaining of surface antigens, using the FoxP3 Buffer Set fromeBioscience according to the manufacturer's recommendations (with smallmodifications in reagent volume to allow staining in 96-well plates).Flow cytometric analysis was performed on a FACSCalibur or FACSCanto IIinstrument (BD), and data was analyzed using FlowJo (TreeStar Inc.,Ashland, Oreg.). Mean fluorescence intensity (MFI) ratios werecalculated by dividing the geometric mean channel fluorescence value ofFoxP3 stained cells by that of isotype-matched control stained cells.Cell sorting was performed on a FACSAria instrument (BD Biosciences).

Epstein-Barr Virus (EBV)-Mediated Transformation of B Cells

Supernatant was collected following 5 days' culture of thelymphoblastoid marmoset cell line B95-8 latently infected with EBV.Virus-containing supernatant was 0.45 μm-filtered and diluted 1/10 withfresh RF-10 containing 1 μg/ml cyclosporine (Novartis PharmaceuticalsAustralia, North Ryde, NSW, Australia). PBMC (2×10⁶ cells/ml) werecultured in this medium for 30 days, changing half of the medium weeklywith fresh RF-10 containing cyclosporine.

T Cell Suppression Assay

CD8⁺ T cells were purified from PBMC using CD8 microbeads (Miltenyi) andlabeled with 1 μM CFSE (Invitrogen) in PBS containing 0.1% FCS at 37° C.for 7 minutes. After washing, T cells were resuspended to 5×10⁵ cells/mlin RF-10 and mixed with stimulator beads (T cell activation/expansionkit; Miltenyi) at 2.5×10⁵ beads/ml. For microwell cultures, 100 μl of Tcell/bead mixture were plated into the wells of a round-bottom 96-wellculture plate and graduated numbers of tumour cells (irradiated 80Gy) orTreg (purified from PBMC using Miltenyi Treg isolation kit according tothe manufacturer's instructions) added in a 100 μl volume.Alternatively, to assess the requirement for direct cell contact, 3×10⁵tumor cells were plated into duplicate wells of a 24-well culture plateand 100 μl of the T cell/bead mixture added either directly to the well(‘co-culture’) or to the upper chamber of a 0.4 μm Transwell® insert(Corning; Lowell, Mass.) (‘separated’). Cells were cultured for 4 daysand then analysed by flow cytometry, using the ‘proliferation’ algorithmin FlowJo to model the percent divided. This value was then used tocalculate percent suppression according to the following formula:100×(1−[test/control]), where ‘control’ was the result of T cellscultured in the absence of any suppressor cells. Tumor cells and Tregwere all allogeneic to the responding T cells.

RNA Isolation and cDNA Synthesis

Total RNA was extracted using the RNeasy® Mini Kit (Qiagen, Hilden,Germany) according to the manufacturer's instructions and immediatelystored at −80° C. Complimentary DNA (cDNA) was synthesized from 1 μgtotal RNA in a 20 μL reaction for 60 min at 42° C. The reactionconsisted of 1 μg random hexamer primers (Promega, Madison, Wis.), 4 mMMgCl₂, 1 mM deoxynucleoside triphosphates (Applied Biosystems, FosterCity, Calif.), 40 units of RNase inhibitor (Promega) and 10 units ofMoloney murine leukemia virus reverse transcriptase (Invitrogen).

PCR, Gel Electrophoresis and DNA Sequencing

In each 25 μl reaction, 1 μl of cDNA was used together with finalconcentrations of 2 mM MgCl₂, 0.2 mM deoxynucleoside triphosphates(Applied Biosystems), 0.625 units of Amplitaq Gold DNA polymerase(Applied Biosystems) and 2 ng of primers (Sigma-Genosys, Castle Hill,NSW, Australia). Primer sequences were as follows:

FOXP3 (forward primer) 5′-GCCCTTGGACAAGGACCCGATG-3′; (SEQ ID NO: 2)FOXP3 (reverse primer) 5′-CATTTGCCAGCAGTGGGTAGGA-3′; (SEQ ID NO: 3)CYCLOPHILIN-A (forward primer) 5′-GTCAGCAATGGTGATCTTCTT-3′; (SEQ ID NO:9) CYCLOPHILIN-A (reverse primer) 5′-GCAGAAAATTTTCGTGCTCTG-3′. (SEQ IDNO: 10)

PCR involved 35 cycles (or 40 cycles, where stated) at 94° C. for 1minute, 66° C. for 1 minute, 72° C. for 1 minute and a final primerextension at 72° C. for 10 minutes. PCR products were resolved using 1%agarose gel electrophoresis. Where required for sequencing, PCR productswere cut from agarose gels and purified with Qiaquick gel extractionkits (Qiagen) according to the manufacturer's instructions. Purified DNAwas sequenced at the Micromon DNA Sequencing Facility (MonashUniversity, VIC, Australia).

Quantitative PCR

Quantitative PCR was performed using an ABI 7700 Prism Sequence Detector(Applied Biosystems). Thermal cycle conditions were set at 50° C. for 2minutes, 95° C. for 10 minutes followed by 40 cycles of 94° C. for 20seconds and 60° C. for 45 seconds. Samples were run in duplicate, andrelative expression of FOXP3 was determined by normalizing to 18Sexpression in order to calculate a fold change in value. FOXP3 primersequences were as follows:

(left primer) 5′-ACCTACGCCACGCTCATC-3′ (SEQ ID NO:7);

(right primer) 5′-TCATTGAGTGTCCGCTGCT-3′ (SEQ ID NO:8) with FOXP3 probenumber 51 from the Roche Universal Probe Library. We calculated therelative mRNA expression using the target threshold (C_(T)) value forreference as a calibrator.

Western Blot

Whole cell lysates from 2×10⁶ cells were prepared by sonication in 100μL lysis buffer containing 0.05% SDS, 50 mM Tris pH 7.5, 5 mM EDTA, 0.5%Sodium Deoxycholate, 150 mM NaCl, 10 mM NaF and protease inhibitors.Samples were heated and approximately 204 per sample (4×10⁵ cellequivalents) were dissolved in 4× NuPAGE LDS Sample Buffer supplementedwith NuPAGE Sample Reducing Buffer (both from Invitrogen) and heated at70° C. for 10 minutes. Equal volumes of lysates were subjected toLDS-PAGE using NuPAGE 4-12% Bis-Tris gels under reducing conditions inMES-SDS running buffer supplemented with NuPAGE Antioxidant (allmaterials from Invitrogen) at 150V. SeeBlue® Plus2 Pre-Stained Standard(10 μl) was loaded into one lane.

Resolved proteins were transferred onto 8×7.5 cm membrane (, Billerica,Mass.) in Trans-blot® Semi-Dry buffer (Bio-Rad Laboratories, Hercules,Calif.) for 15 minutes at 15V constant using NuPAGE transfer buffer(Invitrogen). The membranes were blocked with 5% nonfat dry milk in1×TBS for 1 hour at room temperature, then probed with 2 μg/mlanti-FoxP3 (clone PCH101; eBioscience) overnight at 4° C. After severalwashes with 1×TBS/0.01% Tween 20 (TBS-T), the membranes were incubatedwith a 1:10,000 dilution of HRP-conjugated goat anti-rat-IgG secondary(Chemicon) for 1 hour at room temperature, followed by extensive washeswith TBS-T.

The membranes were treated with a working solution of ECL Plus WesternBlotting Detection kit (Amersham Biosciences, Buckinghamshire, UK) for 5minutes at room temperature. We then used STORM 840 v2005 (AmershamBiosciences) to detect the immunoreactive bands at 100 microns pixelsize with normal sensitivity, followed by analysis via ImageQuant TLSoftware v2003 (Amersham Biosciences). Subsequently, membranes werewashed in TBS-T for 1 hour at room temperature, and re-probed withrabbit antibody to β-actin (Cell Signalling, Danvers, Mass.) diluted1:1,000 overnight at 4° C. After several washes with TBS-T, themembranes were incubated with a 1:20,000 dilution of HRP-conjugatedsheep anti-rabbit-IgG secondary (Chemicon) for 1 hour at roomtemperature, followed by extensive washes with TBS-T. The membranes werethen developed as described above.

Introduction

FoxP3 is a transcription factor that regulates the development andfunction of CD4⁺CD25⁺ T regulatory (T_(reg)) cells. Generally, T_(reg)cells represent approximately 5% of the CD4⁺ T cells in human blood andare essential in maintaining immune homeostasis via T_(reg)cell-mediated immune suppression, and as such, may contribute to tumorimmune escape. We recently observed for the first time that FoxP3expression in melanoma tissue was not only restricted to theinfiltrating T_(reg), but was also expressed within the tumor cells.Therefore, we hypothesized that the expression of FoxP3 duringtumorigenesis may result in tumor immunological tolerance. We verifiedFoxP3 expression in a large number of melanoma cell lines using flowcytometry, reverse-transcription PCR and Western blot. Furthermore, weextended the study with tumor cell lines from other types ofmalignancies and demonstrated that the majority expressed FoxP3. Incontrast, we showed that normal primary cell lines did not expressFoxP3, supporting the association of FoxP3 expression withtumorigenesis. Meanwhile, we discovered a novel third splice isoform ofFoxP3, which was not only expressed in tumour cells but also in thebrain and testis, suggesting that these tissues may establish an immuneprivilege-like site by expressing FoxP3. In conclusion, our data revealthat tumor cells express the transcription factor FoxP3, which mayprovide a survival advantage by setting in motion an immunosuppressivegenetic program that inhibits the generation of an effective anti-tumorimmune response.

Full Coding Sequence of FoxP3 from Database (Accession NumberNM_(—)014009):

SEQ ID NO:1 (shown without introns, but indicating the location andlength of introns)

-   -   non-quantitative PCR primer positions are indicated in bold    -   real-time PCR primer positions are underlined    -   start positions of siRNA sequences are indicated in italics and        underlining

FOXP3 > hg2B_knownGene_NM_014009 range = chrX:48994354-49008232 (UTR)GCACACACTCATCGAAAAAAATTTGGATTATTAGAAGAGAGAGGTCTGCGGCTTCCACACCGTACAGCGTGGTTTTTCTTCTCGGTATAAAAGCAAAGTTGTTTTTGATACGTGACAGTTTCCCACAAGCCAGGCTGATCCTTTTCTGTC AGTCCACTTCACCAAGIntron 6238 bps (EXON 1)CCTGCCCTTGGACAAGGACCCGATGCCCAACCCCAGGCCTGGCAAGCCCTCGGCCCCTTCCTTGGCCCTTGGCCCATCCCCAGGAGCCTCGCCCAGCT G GAGGGCTGCACCCAAAGCCTCAGACCTGCTGGGGGCCCGGGGCCCAGGGGGAACCTTCCAGGGCCGAGATCTTCGAGGCGGGGCCCATGCCTCCTCTTCTTCCTTGAACCCCATGCCACCATCGCAGCTGCAG Intron 527 bps (EXON 2)CTGCCCACACTGCCCCTAGTCATGGTGGCACCCTCCGGGGCACGGCTGGGCCCCTTGCCCCACTTACAGGCACTCCTCCAGGACAGGCCACATTTCATGC ACCAG Intron 98 bps(EXON 3) CTCTCAACGGTGGATGCCCACGCCCGGACCCCTGTGCTGCAGGTGCACCCCCTGGAGAGCCCAGCCATGATCAGCCTCACACCACCCACCACCGCCACTGGGGTCTTCTCCCTCAAGGCCCGGCCTGGCCTCCCACCTG Intron 424 bps (EXON 4)GGATCAACGTGGCCAGCCTGGAATGGGTGTCCAGGGAGCCGGCACTGCTCTGCACCTTCCCAAATCCCAGTGCACCCAGGAAGGACAG Intron 69 bps (EXON 5)CACCCTTTCGGCTGTGCCCCAGAGCTCCTACCCACTGCTGGCAA A TGGTGTCTGCAAGTGGCCCGGATGTGAGAAGGTCTTCGAAGAGCCAGAGGACTTC CTCAA Intron 944 bps(EXON 6) GCACTGCCAGGCGGACCATCTTCTGGATGAGAAGGGCAGGGCACAATGTCTCCTCCAGAGAGAGATGGTACAGTCTCTGGAGCAGCAG Intron 205 bps (EXON 7)CTGGTGCTGGAGAAGGAGAAGCTGAGTGCCATGCAGGCCCACCTGGCTGGGAAAATGGCACTGACCAAGGCTTCATCTGTG Intron 1361 bps (EXON 8)GCATCATCCGACAAGGGCTCCTGCTGCATCGTAGCTGCTGGCAGCCAAGGCCCTGTCGTCCCAGCCTGGTCTGGCCCCCGGGAGGCCCCTGACAGCCTGTTTGCTGTCCGGAGGCACCTGTGGGGTAGCCATGGAAACAGCACATTCCCA G Intron 714 bps(EXON 9) AGTTCCTCCACAACATGGACTACTTCAAGTTCCACAACATGCGACCCCCTTTCACCTACGCCACGCTCATCCGCTGG Intron 1360 bps (EXON 10)GCCATCCTGGAGGCTCCAGAGAAGCAGCGGACACTCAATGAGATCTACCACTGGTTCACACGCATGTTTGCCTTCTTCAGAAACCATCCTGCCACCTGGA AG Intron 180 bps(EXON 11) AACGCCATCCGCCACAACCTGAGTCTGCACAAGTGCTTTGTGCGGGTGGAGAGCGAGAAGGGGGCTGTGTGGACCGTGGATGAGCTGGAGTTCCGCAAGAAACGGAGCCAGAGGCCCAGCAGGTGTTCCAACCCTACACCTGGCCCCTGACCTCAAGATCAAGGAAAGGAGGATGGACGAACAGGGGCCAAACTGGTGGGAGGCAGAGGTGGTGGGGGCAGGGATGATAGGCCCTGGATGTGCCCACAGGGACCAAGAAGTGAGGTTTCCACTGTCTTGCCTGCCAGGGCCCCTGTTCCCCCGCTGGCAGCCACCCCCTCCCCCATCATATCCTTTGCCCCAAGGCTGCTCAGAGGGGCCCCGGTCCTGGCCCCAGCCCCCACCTCCGCCCCAGACACACCCCCCAGTCGAGCCCTGCAGCCAAACAGAGCCTTCACAACCAGCCACACAGAGCCTGCCTCAGCTGCTCGCACAGATTACTTCAGGGCTGGAAAAGTCACACAGACACACAAAATGTCACAATCCTGTCCCTCAC

Example 1 FoxP3 is Expressed by Both Lymphocytes and Tumor Cells inMetastatic Melanoma Tissue

With the aim of characterizing the frequency and localization of Treg inmelanoma, we performed immunohistochemistry (IHC) on metastatic melanomatissue sections using a polyclonal anti-FoxP3 antibody. Surprisingly, inaddition to the expected staining of cells with lymphocyte morphology(small, round, dense nucleus and little cytoplasm), staining was alsooccasionally apparent in cells which had several morphological featuresof tumor cells, such as a large, irregular nucleus and abundantcytoplasm (FIG. 1 a). Although unexpected, this staining appears to bespecific, given the nuclear localization of the signal and the lack ofstaining with control rabbit IgG (not shown). Furthermore, this is notan isolated phenomenon, as FoxP3⁺ tumor cells were detectable in fouradditional biopsy specimens from different patients and various sites ofmetastasis.

This preliminary analysis therefore suggested that a proportion ofFoxP3⁺ cells in melanoma tissue represent the tumor cells themselves,not Treg. To definitively identify these FoxP3⁺ cells as melanoma cells,two-color IHC was performed using antibodies to both FoxP3 and Melan-A,a specific marker of melanocytic differentiation (21). As shown in FIG.1 b, FoxP3⁺ cells were readily identified within Melan-A⁺ tumor cellislands, whereas infiltrating Treg were located outside of these islandsand lacked staining for Melan-A. These results therefore provide furtherevidence that, in addition to Treg, melanoma cells can also expressFoxP3.

To our knowledge, the expression of FoxP3 by cells outside of the T celllineage has not been previously reported, except in pancreatic carcinomacells (Hinz et al., Cancer Res. 2007; 67(17):8344-50; Hinz, S;Pagerols-Raluy, L; Ammerpohl, O; Oberg, H H; Wesch, D; Kabelitz, D;Gruetzman, R; Faendrich, F; Kalthoff, H., Significance of the expressionof the Treg marker FoxP3 in pancreatic carcinoma cells with regard to animmunomodulatory action on nave T cells. 123rd Congress of the GermanSociety for Surgery, Berlin; 2-5 May, 2006).

To confirm the immunohistochemical results of our IHC studies, wegenerated cell suspensions from disaggregated melanoma tissue andanalyzed them using 6-color flow cytometry, using a hierarchical gatingstrategy to unambiguously identify both melanoma cells and CD4⁺ T cellswithin the mixed cell population (FIG. 2). To identify melanoma cells, Tcells were first excluded on the basis of forward and side scatter andthen by gating out CD3⁺ and CD4⁺ events. Endothelial cells and tissuefibroblasts were excluded by gating out CD31⁺ and CD90⁺ events,respectively, and melanoma cells within the remaining population wereidentified by staining for MCSP (melanoma chondroitin sulfateproteoglycan), a marker widely expressed in melanoma (22). Fluorescenceminus one (FMO) isotype-matched negative controls were used to assessthe level of background staining within this population, and thispattern compared to staining with anti-FoxP3. Generally, the addition ofanti-FoxP3 produced a shift of the entire MCSP⁺ population compared tothe control; the magnitude of this shift varied greatly, ranging frombarely detectable to >1 log shift. In addition, many samples had a smallsub-population of FoxP3^(bright) cells that clearly expressed muchhigher levels of FoxP3 than the bulk population. The examples shown inFIG. 2 a-b illustrate these different patterns; the sample in part (a)demonstrates only a slight shift of the entire population but a distinctpopulation of FoxP3^(bright) cells, while the sample in part (b) wascharacterized by a prominent shift of the entire population but nodistinct subset of FoxP3^(bright) cells. For the 7 samples analyzed, themean proportion of FoxP3^(bright) cells was 0.1±0.09% (SD, range0-0.24%). This population likely corresponds to the scattered FoxP3⁺melanoma cells identified in IHC analysis of tissue sections.

The proportion of Treg was also determined for each sample by gating onCD3⁺ CD4⁺ cells within the lymphocyte gate (FIG. 2 a). Similar toprevious studies (9, 10), the proportion of CD4⁺ T cells stainingpositive for FoxP3 in melanoma tissue was remarkably high, with a meanvalue of 21.1±14.3% (range 5.8-41.1%). These FoxP3⁺ T cells were alsoCD25⁺ and CD127^(neg/lo), thereby confirming their identity as Treg (notshown). No obvious correlation was observed between the proportion ofTreg and the proportion of FoxP3^(bright) melanoma cells.

In order to confirm that melanoma cells expressed FOXP3 transcripts, thedisrupted tumor tissue was subject to high-stringency cell sorting topurify the melanoma cells (identified as MCSP⁺ CD3⁻ CD4⁻ CD31⁻ CD90⁻)and these cells were subject to RT-PCR analysis (FIG. 2 c). PCR usingprimers specific for the housekeeping gene CYCLOPHILIN-A (CYPA) produceda band of the expected size for both specimens, confirming the integrityof the cDNA. PCR using FOXP3 primers produced a pattern of bandssimilar—but not identical—to that observed for CD4+Treg (see later),thus confirming the presence of FOXP3 transcripts in sorted melanomacells. Importantly, analysis of the sorted populations confirmed thatthey were >98% MCSP⁺ and that the level of T cell contamination was<0.005%. PCR amplification using primers for CD4 revealed no product forsample #2 and, while a faint band was detectable for sample #1, no Tcells were detected by flow cytometry, suggesting that these CD4transcripts likely originate from contaminating DCs ormonocyte/macrophages, not Treg. Thus, FOXP3 transcripts can be amplifiedfrom pure, freshly isolated melanoma cells, providing further evidencethat these cells can express FoxP3.

Example 2 FoxP3 is Widely Expressed by Melanoma Cell Lines

The results presented thus far demonstrate, using a variety of methods,that cells with the morphology and surface marker phenotype of melanomacan express FoxP3. However, the identification of melanoma cells withina mixed population using these criteria is not unequivocal. Furtherconfirmation of FoxP3 expression in melanoma cells was obtained byanalyzing a panel of established melanoma cell lines by flow cytometry(FIG. 3) after staining with anti-FoxP3 mAb. The melanoma cell lineshown in FIG. 3 a (SK-Mel-14) was uniformly positive for FoxP3, althoughthe intensity of staining was not quite as high as for CD4⁺ CD25⁺ Tcells. Staining of freshly isolated blood NK cells and monocytes wasnegative, as expected.

Staining for FoxP3 on additional melanoma cell lines is summarized inFIG. 3 b. For all cell lines analyzed, staining with anti-FoxP3 resultedin a shift in the fluorescence of the entire population compared to theisotype control, but the magnitude of this shift varied substantially.In order to quantify the intensity of staining, the mean fluorescenceintensity (MFI) was determined following staining with anti-FoxP3 orisotype control and a ratio of the two values calculated. Thiscalculation was necessary to normalize the different levels ofbackground fluorescence amongst the various cell lines. The samecalculation was also performed for a range of negative control cells(freshly isolated blood NK cells and monocytes, and 7-day culturedmonocyte-derived dendritic cells) in order to establish the backgroundMFI ratio (indicated by a dotted line). The majority of melanoma celllines had MFI ratios well above this background level, although theintensity of FoxP3 expression varied considerably and a small proportionof cell lines had ratios only slightly above background. In contrast,cultured normal epidermal melanocytes did not express detectable levelsof FoxP3. Expression of FoxP3 protein was further confirmed in melanomacell lines using Western blotting (FIG. 3 c). As previously described,lysates from Treg cells ran as a closely spaced doublet, correspondingto full-length FoxP3 and a splice variant lacking exon 2, respectively(14, 15). In melanoma cells, a band corresponding to full-length FoxP3(but not the Δ2 variant) was also readily detectable. Thus, FoxP3 iswidely expressed in melanoma cell lines (but not normal melanocytes);however, the intensity of expression is variable and a small number ofmelanoma cell lines express only borderline levels of FoxP3.

Example 3 The FOXP3 Gene is Expressed in Melanoma Cells as ThreeDistinct mRNA Variants, One of which is Predicted to Encode a NovelProtein

To confirm FOXP3 gene expression in melanoma cells, RNA was extractedfrom a panel of melanoma cell lines and used to generate cDNA by reversetranscription, which was then subject to PCR using primers specific forFOXP3 or the housekeeping gene CYP-A (cyclophilin-A). PCR products couldbe readily detected following amplification using FOXP3-specific primers(35 cycles), confirming that melanoma cell lines express FOXP3 mRNA(FIG. 4 a).

Previous reports have demonstrated that, in Treg, FOXP3 mRNA isexpressed as two variants: full-length and an alternatively splicedversion lacking exon 2 (Δ2) (11, 15, 23). Using our primers, these twoproducts would be expected to result in band sizes of 608 and 503 bp,respectively, and for CD4⁺ T cells these two bands were observed asexpected (FIG. 4 a). For melanoma cells, however, an additional band(˜100 bp smaller than the Δ2 product) was frequently detected which wasnot apparent in Treg. To better visualize this band, the PCR wasrepeated for selected cell lines at 40 cycles instead of 35 cycles (FIG.4 b). This analysis confirmed the presence of a third PCR product inmelanoma cells which was absent from both freshly purified CD4⁺ T cellsand a Treg cell line expanded in culture for several weeks. Sequencingof this third band from one melanoma cell line (LM-Mel-34) revealed thatthis product was lacking both exons 2 and 3, and therefore correspondsto a novel FOXP3 mRNA variant (Δ2,3; FIG. 4 c). As expected, sequencingof the upper (608 bp) band confirmed that it was identical to thepublished sequence for fill-length FOXP3.

The previously described A2 splice variant contains an in-frame excisionof exon 2 (105 bp), which is predicted to result in removal of part ofthe repressor domain of the normal FoxP3 protein without affectingsequences downstream of the second exon (11, 15). In contrast, the novelΔ2,3 isoform contains a 244 bp excision which is expected to result in atranslation frame-shift.

The three isoforms of FoxP3 mRNA amplified and sequenced are as follows:

Full-length (608 bps) (SEQ ID NO: 4) EXON 1 (229bps)GCCCTTGGACAAGGACCCGATGCCCAACCCCAGGCCTGGCAAGCCCTCGGCCCCTTCCTTGGCCCTTGGCCCATCCCCAGGAGCCTCGCCCAGCTGGAGGGCTGCACCCAAAGCCTCAGACCTGCTGGGGGCCCGGGGCCCAGGGGGAACCTTCCAGGGCCGAGATCTTCGAGGCGGGGCCCATGCCTCCTCTTCTTCCTTGAACCCCATGCCACCATCGCAGCTGCAG EXON 2 (105 bps)CTGCCCACACTGCCCCTAGTCATGGTGGCACCCTCCGGGGCACGGCTGGGCCCCTTGCCCCACTTACAGGCACTCCTCCAGGACAGGCCACATTTCATGC ACCAG EXON 3 (139bps) CTCTCAACGGTGGATGCCCACGCCCGGACCCCTGTGCTGCAGGTGCACCCCCTGGAGAGCCCAGCCATGATCAGCCTCACACCACCCACCACCGCCACTGGGGTCTTCTCCCTCAAGGCCCGGCCTGGCCTCCCACCTG EXON 4 (88 bps)GGATCAACGTGGCCAGCCTGGAATGGGTGTCCAGGGAGCCGGCACTGCTCTGCACCTTCCCAAATCCCAGTGCACCCAGGAAGGACAG EXON 5 (47 bps)CACCCTTTTCGGCTGTGCCCCAGAGCTCCTACCCACTGCTGGCAAATG Δ2 splice variant (503bps) (SEQ ID NO: 5) EXON 1 (229 bps)GCCCTTGGACAAGGACCCGATGCCCAACCCCAGGCCTGGCAAGCCCTCGGCCCCTTCCTTGGCCCTTGGCCCATCCCCAGGAGCCTCGCCCAGCTGGAGGGCTGCACCCAAAGCCTCAGACCTGCTGGGGGCCCGGGGCCCAGGGGGAACCTTCCAGGGCCGAGATCTTCGAGGCGGGGCCCATGCCTCCTCTTCTTCCTTGAACCCCATGCCACCATCGCAGCTGCAG EXON 3 (139 bps)CTCTCAACGGTGGATGCCCACGCCCGGACCCCTGTGCTGCAGGTGCACCCCCTGGAGAGCCCAGCCATGATCAGCCTCACACCACCCACCACCGCCACTGGGGTCTTCTCCCTCAAGGCCCGGCCTGGCCTCCCACCTG EXON 4 (88 bps)GGATCAACGTGGCCAGCCTGGAATGGGTGTCCAGGGAGCCGGCACTGCTCTGCACCTTCCCAAATCCCAGTGCACCCAGGAAGGACAG EXON 5 (47 bps)CACCCTTTCGGCTGTGCCCCAGAGCTCCTACCCACTGCTGGCAAATG Δ2, 3 splice variant(364 bps) (SEQ ID NO: 6) EXON 1 (229 bps)GCCCTTGGACAAGGACCCGATGCCCAACCCCAGGCCTGGCAAGCCCTCGGCCCCTTCCTTGGCCCTTGGCCCATCCCCAGGAGCCTCGCCCAGCTGGAGGGCTGCACCCAAAGCCTCAGACCTGCTGGGGGCCCGGGGCCCAGGGGGAACCTTCCAGGGCCGAGATCTTCGAGGCGGGGCCCATGCCTCCTCTTCTTCCTTGAACCCCATGCCACCATCGCAGCTGCAG EXON 4 (88 bps)GGATCAACGTGGCCAGCCTGGAATGGGTGTCCAGGGAGCCGGCACTGCTCTGCACCTTCCCAAATCCCAGTGCACCCAGGAAGGACAG EXON 5 (47 bps)CACCCTTTCGGCTGTGCCCCAGAGCTCCTACCCACTGCTGGCAAATG

The predicted amino acid sequence is shown in FIG. 4 d; this sequence isidentical to FoxP3 in the N-terminal portion encoded by exon 1, but thisregion is followed by a 103aa sequence with no significant homology toFoxP3 (or any other sequence in the public databases) and a prematurestop codon, resulting in a protein that is approximately half the sizeof FoxP3.

Example 4 FoxP3 is Also Expressed in Cell Lines Derived from Other Typesof Solid Tumor

Given that FoxP3 was widely expressed in melanoma cell lines, we wereinterested to determine if cell lines derived from other types of solidtumor also expressed FoxP3. Accordingly, an extensive panel of tumorcell lines was examined for FoxP3 expression by flow cytometry; thispanel comprised 3-4 cell lines each from colon cancer, lung cancer,breast cancer, prostate cancer, glioblastoma, renal cell carcinoma andbladder cancer (FIG. 5 a). As per the melanoma cell lines, the intensityof FoxP3 expression was determined relative to isotype control stainingand calculated as an MFI ratio. The grey region indicates the meanbackground MFI ratio as determined in FIG. 3 b; any measurement fallingwithin, or very close to, this region cannot be considered positive forFoxP3.

This analysis revealed that at least one cell line from each type oftumor expressed readily detectable levels of FoxP3. Some, such asprostate cancer and colon cancer, were uniformly positive, whereasothers, such as breast cancer, appeared to express FoxP3 lessfrequently. However, given the small sample size for each type ofcancer, these differences cannot be considered conclusive. Early passagecultures of normal fibroblasts (derived from dermis or foreskin) lackedconvincing staining for FoxP3, suggesting that the expression of FoxP3is restricted to malignant cell lines. Interestingly, however, extendedculture of fibroblasts did eventually result in induction of FoxP3expression (FIG. 5 a). The mechanism responsible for this observation isunclear at present, although it is possible that FoxP3 is induced innormal tissue cells as they approach replicative senescence, or inresponse to extended culture under non-physiological conditions. Supportfor the latter possibility comes from a comparison of FoxP3 expressionin matched melanoma biopsies and cell lines derived from them, whichrevealed a much higher frequency of FoxP3⁺ cells in the cell line thanthe original tissue (data not shown). However, it is unclear at presentwhether this reflects genuine modulation of FoxP3 expression in cultureor selective expansion of rare FoxP3⁺ melanoma cells.

To confirm expression of FOXP3 transcripts, one cell line from each typeof cancer was selected on the basis of unequivocal expression of FoxP3protein by flow cytometry and analyzed by RT-PCR. As shown in FIG. 5 b,each cell line tested positive for FOXP3, and several cell lines alsoexpressed the Δ2,3 isoform described in FIG. 4. Thus, the expression ofFoxP3 in tumor cell lines is not restricted to melanoma cells.

Example 5 A Novel Isoform of FoxP3 can be Identified in Some Tumor CellLines as Well as Normal Testis and Brain Tissue

As mentioned above, it was observed that some tumor cell lines expressedthree distinct foxp3-derived transcripts, instead of the usual two asdetected in T_(reg) (see FIGS. 4 and 6). Further analysis of a panel ofRNAs derived from normal tissues (Clontech) revealed that this third wasalso clearly detectable in adult testis and brain (but not ovary), aswell as fetal brain tissue (FIG. 8). All other healthy tissue examinedlacked this third band, although the two upper bands were oftenobserved, presumably due to the presence of T_(reg) in the vasculature.Sequencing of this band revealed that it lacked both exons 2 and 3 ofthe full-length transcript. To our knowledge, this isoform of foxp3 hasnot been previously described.

In order to confirm the unexpected expression of foxp3 in testis, tissuesections were stained by immunohistochemistry (using the polyclonalanti-FoxP3 antiserum as used in FIG. 1). This analysis revealed strongFoxP3 expression in the germ cells near the basement membrane, whilemore differentiated cells lacked detectable FoxP3 expression (FIG. 9A).Interestingly, this expression pattern is virtually identical to thatobserved for cancer-testis (CT) antigens such as NY-ESO-1 (FIG. 9B).Thus, FoxP3 has a very similar distribution pattern to that of a CTantigen (being expressed in cancer and testis), raising the intriguingpossibility of hierarchical or linked gene expression patterns.

Example 6 Expression of Foxp3 by Melanoma Cell Lines can be Modulated bysiRNA-Mediated Gene Knockdown

A small interfering RNA (siRNA) approach was used to knock-down foxp3gene expression in melanoma cell lines. Knock-down of foxp3 geneexpression was achieved using a commercially available siRNA reagent(FoxP30N-TARGETplus SMARTpool®, from Dharmacon, cat#L-009307-00). Thisreagent consists of a pool of four siRNAs that have been modified toreduce off-target effects.

The approximate 5′ start positions for the four siRNAs were provided byDharmacon (which are indicated in underlined italics in the full-lengthsequence). The FoxP3 exons that are targeted are as follows:

siRNA start position exon Duplex 6: 775 5 Duplex 7: 265 1 Duplex 8: 127010 Duplex 9: 1315 10

Real-time (quantitative) PCR was performed using the following FoxP3primers:

Sense: 5′-ACCTACGCCACGCTCATC-3′ (SEQ ID NO: 7) Antisense:5′-TCATTGAGTGTCCGCTGCT-3′ (SEQ ID NO: 8)

Preliminary results using real-time (quantitative) PCR revealed anapproximately 75% reduction in gene expression following transfectionwith an siRNA targeted to foxp3, compared to that observed followingtransfection with a non-targeting control (FIG. 10). This thereforeappears to be a valid approach by which to address the function of FoxP3in tumor cells, which is a focus of additional experiments.

Example 7 Comparison of FoxP3 and NY-ESO-1 Expression in Tumour CellLines

The expression of FoxP3 and NY-ESO-1 was compared in tumour cell lines.A summary of the PCR results for the LM-MeI cell line series ispresented in Table 1 below. There are only 2 melanoma cell lines thatlacked FoxP3 expression (LM-Mel-7 and LM-Mel-47), as tested by RT-PCR.Both of these cell lines are negative for NY-ESO-1 expression by RT-PCR.However, we have had some recent data that may contradict the apparentlack of FoxP3 expression in LM-Mel-47, and are resolving thisdiscrepancy.

TABLE 1 FoxP3 and NY-ESO-1 expression in melanoma cell lines Cell line(LM-Mel #) ESO FoxP3  1a yes yes  5 no yes  6 no yes  7 no no  8 no yes 9 no yes 10 no yes 13 no yes 14 yes yes 17 yes yes 19 no yes 20 no yes22 no yes 24 no yes 25 no yes 26 no yes 27 no yes 28 yes yes 33 no yes34 yes yes 36 yes yes 37 no yes 38 no yes 39 no yes 40 yes yes 41 yesyes 42 yes yes 43 no yes 44 yes yes 45 no yes 46 no yes 47 no no

The only other tumour cell lines to show low/absent FoxP3 expression sofar are two bladder cancer lines. HT1197 is negative for ESO by RT-PCR,and negative for FoxP3 by both PCR and flow cytometry. The story forHT1376 is a little more complicated. Using freshly prepared RNA, thiscell line tested negative for FoxP3 by PCR, and showed only marginalstaining for FoxP3 by flow cytometry. However, RNA from this cell linethat was prepared several years ago tested positive for both FoxP3 andESO. It is possible that the expression of FoxP3 was lost with extendedculture.

ESO expression after siRNA-mediated Foxp3 knockdown also is tested.

Thus far, it appears that all FoxP3-negative cell lines also lack ESOexpression, although many FoxP3-positive cell lines also lack ESOexpression. One could possibly make the case that FoxP3 is necessary butnot sufficient for expression of ESO.

Example 8 FoxP3 Expression is Induced During EBV-Mediated B CellTransformation in Vitro and In Vivo

Infection of B cells with Epstein-Barr virus (EBV) inducestransformation and can therefore serve as an in vitro model for B celllymphoma formation. We used this model to investigate whethertransformation is associated with de novo induction of FoxP3 expression.Peripheral blood mononuclear cells (PBMC) from 4 healthy donors wereinfected with EBV in vitro and cultured in the presence of cyclosporineto block the expansion of EBV-specific T cells. When analyzed by flowcytometry after 30 days' culture, a distinct population of cells withhigh forward and side scatter characteristics was evident, the majorityof which expressed CD19 and MHC class II, corresponding to thetransformed B cell blasts (FIG. 6 a). In addition, a population of smalllymphocytes remained, and while many of these were T cells, a fractionwere CD19⁺ and therefore likely represent resting B cells that haveescaped transformation. This population was not evident in moreestablished EBV-transformed B cell lines (not shown), suggesting that itis gradually diluted out with extensive passage.

Prior to culture, CD19⁺ B cells did not express detectable FoxP3, asexpected. After 30 days' culture, the small B cells still lacked FoxP3expression whereas the transformed B cell blasts had clearlyup-regulated FoxP3 expression (FIG. 6 b). A more detailed time-courseanalysis (FIG. 6 c) revealed that the blasts were first detectable ataround day 15 of culture, at which time they had already begun toup-regulate FoxP3. With further culture, the level of FoxP3 expressionprogressively increased until the last day of analysis (day 30). Incontrast, expression of FoxP3 in the small B cells remained low toundetectable throughout the culture period, arguing against anon-specific induction of FoxP3 in cultured B cells. After furtherexpansion to generate larger cell numbers, expression of FOXP3 mRNA wasconfirmed for one of these cultures by RT-PCR (not shown).

Post-transplant lymphoproliferative disorder (PTLD) is a complication ofsolid organ and bone marrow transplantation in which B cell lymphomasdevelop following EBV-induced transformation of B cells (24). Given thattransformation of B cells in vitro with EBV appeared to induce FoxP3expression, we hypothesized that B cell lymphomas from PTLD patientswould also express FoxP3. To test this, cryopreserved cell samples froma patient who developed PTLD following a heart transplant were assessedfor FoxP3 expression (FIG. 6 d). Normal CD19⁺ B cells within thepatient's PBMC did not express FoxP3, as expected. However, whendisaggregated lymphoma tissue from the same patient was analyzed, adistinct population of FoxP3⁺ CD19⁺ B cells could be detected. Thesewere clearly not Treg, as CD4⁺ T cells were gated out of the analysis.Interestingly, the FoxP3⁺ B cells expressed a lower level of CD19 thanthe FoxP3⁻ B cells, although the significance of this observation isunclear at present.

Example 9 FoxP3-Expressing Tumor Cell Lines Suppress T CellProliferation

Considering the central role that FoxP3 plays in the development andfunction of Treg, we hypothesized that expression of FoxP3 by tumorcells may endow them with Treg-like activity, enabling them to suppressthe generation of anti-tumor cytotoxic T cell (CTL) responses. To testthis concept, CD8⁺ T cells were purified from PBMC, labeled with CFSEand co-cultured with FoxP3-expressing tumor cells or freshly isolatedTreg in the presence of a polyclonal stimulus to induce T cellproliferation (FIG. 7 a-b). As expected, Treg induced a dose-dependentinhibition of T cell proliferation. Moreover, three out of four tumorcell lines tested (two melanoma lines and one breast cancer line) alsosignificantly suppressed T cell proliferation. Of note, the suppressioninduced by tumor cell lines was generally even more potent than thatinduced by Treg; for example, SK-Mel-14 almost completely abolished Tcell proliferation even at a tumor:T cell ratio of 2:1. Similar resultswere observed using CD4⁺ T cell responders (not shown).

A characteristic feature of the suppression mediated by Treg is that itis dependent on close contact between Treg and the responding T cells(5). To test if this was also the case for tumor cells, duplicatecultures were set up in which the tumor cells and the responding T cellswere either placed in the same well or were separated by asemi-permeable Transwell® membrane (FIG. 7 c-d). The suppressionmediated by SK-Mel-14 and MDA-MB-468 cell lines was clearly reduced whenthe tumor cells were physically separated from the responding T cells,indicating that the suppressive effect of these cells is primarilycontact dependent. In contrast, the suppression mediated by LM-Mel-26was only slightly affected by physical separation, suggesting that thiscell line uses suppressive mechanisms that are not dependent on directcontact with the target cells, such as the production ofimmunosuppressive cytokines. In keeping with FIG. 7( a), LM-Mel-14 wasnot suppressive under either condition.

Example 10 FOXP3 Knockdown in Melanoma Cell Lines Reagents

FOXP3 positive, HLA-A2, HLA-B7 and HLA-C3 positive melanoma cell linesare selected:

-   -   HLA-A2+HLA-B7: LM-Mel-1a, LM-Mel-5, LM-Mel-26    -   HLA-A2+HLA-C3: LM-Mel-19, LM-Mel-31, LM-Mel-33, LM-Mel-34    -   HLA-C3 alone: LM-Mel-14, LM-Mel-28

FOXP3 siRNA plus relevant controls are obtained from commercialsuppliers, such as Ambion (via Geneworks in Adelaide, Australia), IDT,and Dharmacon. FOXP3-AS2 antisense oligonucleotide can be obtained fromMWG Biotech.

Lipofectamine/OptiMEM are used as transfection reagents.

Knockdown

Trial ˜3× siRNA, compare to ubiquitous positive and scrambled negativecontrols.

Relative knockdown is measured by FACS, RT-PCR and Western analyses.

Effect of FOXP3 Knockdown on Melanoma Cell Line Growth

The following assays are run to observe the effects of FOXP3 knockdown:

Proliferation by MTS assay

Clonogenicity by CFU in agar

Morphology and antigen expression by PCR and IHC

-   -   CTAg and differentiation antigens    -   Class I/II, GITR, proteasome components

Immunological Consequences of FOXP3 Inhibition in Melanoma Cell Lines

The immunological effects of FOXP3 knockdowns are assayed by:

-   -   Cytokine release by FOXP3 knockdown melanoma cells, measured        using a BD Cytometric Bead Array.    -   Cytotoxicity, measured using calcein release assay, inhibition        of clonogenicity, and CCIA.    -   In vitro stimulation of CD4/CD8 T-cells by melanoma cells is        measured by ICS for IFN-γ and T-cell proliferation by CFSE.    -   Using melanoma antigen specific CD8 T-cells: CGW Melan-A 5-10%        specific after one stimulation; A2, B7 and C3 restricted        NY-ESO-1 specific T-cells; and EBV, FLU epitope controls.

In Vivo Immunological Consequences of FOXP3 Inhibition in Melanoma CellLines

An inducible shRNA transfection construct for FOXP3 is developed.

Tumourigenicity in mouse model is tested.

FOXP3 inhibition influence on tumour formation and immune response toadoptively transferred melanoma specific human CD8 T-cells is tested.

Effect of Drugs on FOXP3 Expression in Melanoma

If FOXP3 is immunologically or biologically relevant in melanoma celllines, the effect of pharmacological manipulation of melanoma cell linesis assessed, as follows.

-   -   In vitro: proliferation, clonogenicity, antigen expression as        above.    -   In vivo: tumourigenicity, and adoptively transferred immune        response to melanoma xenografts in drug treated animals.

Examples of agents that may influence CD4+CD25+FOXP3+ T-regs include:

-   -   a. Cyclophosphamide (Motoyoshi et al., Oncol Rep. 2006 July;        16(1):141-6.    -   b. IL-2 (Ahmadzadeh and Rosenberg, Blood. 2006 Mar. 15;        107(6):2409-14; Cesana et al, J Clin Oncol. 2006 Mar. 1;        24(7):1169-77.)    -   c. Interferon (Putheti, J Clin Immunol. 2004 March;        24(2):155-61.)    -   d. Mycophenlate mofetil, 1,25-vitamin-D3 (Gregori, J Immunol.        2001 Aug. 15; 167(4):1945-53.)    -   e. Fludarabine (Beyer et al, Blood. 2005 Sep. 15;        106(6):2018-25.)

Example 11 Western Blotting of Melanoma Cell Line Lysates Using anAntibody Raised Against the Δ3,4 Variant

A 15 amino acid peptide (SSRERWYSLWSSSWC; SEQ ID NO:13) was synthesizedcorresponding to a region of the frame-shifted portion of the variantFoxP3 polypeptide (which bears no similarity to wild-type FoxP3). Thispeptide was conjugated to the carrier KLH (keyhole limpet hemocyanin)and used to immunize rabbits, and IgG was purified from the immune serumby Protein A chromatography. This antiserum was used at a finalconcentration of 2 μg/ml to probe lysates prepared from three differentmelanoma cell lines, all of which express the Δ3,4 FoxP3 variant byRT-PCR. Note that the predicted molecular weight of the variant isapproximately 17 kD. FIG. 11 a demonstrates the presence of a band ofthe expected size for all three melanoma cell lines tested.

To demonstrate the specificity of the reaction, the antibody waspre-blocked for 2 hours at room temperature with either the peptide usedfor immunization or an irrelevant peptide control (0.2 μg/ml). Theantibody/peptide mixture was then used for Western blotting and banddensity was determined using ImageQuaNT software. This analysis is shownin FIG. 11 b, and demonstrates that the band intensity is greatlyreduced after blocking with the specific peptide.

Example 12 T Cell Responses to the Δ3,4 Variant in a Patient withAdvanced Melanoma

A panel of overlapping 18 amino acid peptides was synthesized coveringthe entire predicted protein sequence of the Δ3,4 variant. Patientperipheral blood mononuclear cells (PBMC) were cultured with eachpeptide for 11 days in the presence of 25 IU/ml IL-2 and thenre-stimulated with the same peptide for 4 hours in the presence ofBrefeldin-A (see Jackson et al, J. Immunol. Methods. 291: 51-62). Thecells were then stained with fluorochrome-conjugated antibodies to CD4and CD8, fixed with 1% formaldehyde and incubated overnight withFITC-conjugated anti-IFN-γ in the presence of 0.2% saponin. Cells werethen subject to flow cytometric analysis, gating on either CD8⁺ (FIG. 12a) or CD4⁺ (FIG. 12 b) T cells.

Discussion

Using a wide variety of approaches, the present study demonstrates,using a variety of approaches, that the FoxP3 transcription factor isexpressed by melanoma cells, virally-transformed B cells and cell linesderived from a variety of solid tumors. This observation is particularlyinteresting as it was previously believed that FoxP3 expression wasstrictly limited to T cells (19, 20). A study by Chang et al in 2005 hadoriginally suggested that FoxP3 was also expressed by thymic epitheliumin the mouse (25), but this has since been shown not to be the case(26). A recent report demonstrated that FOXP3 is a tumor suppressor genein both mouse and human breast cancer (27). The authors detectedexpression of FoxP3 protein in normal breast epithelium, and showed thatexpression was lost or reduced in breast cancer due to reduced levels ofFOXP3 transcription or deletion of the FOXP3 locus. As a result,FoxP3-mediated repression of the HER-2/ErbB2 oncogene is lifted, whichis likely to be an important contributing factor to carcinogenesis.Interestingly, the authors also detected novel FOXP3 splice variants inbreast cancer cells. One of these is referred to as lacking exons 3 and4, resulting in a frame-shift beginning at codon 70 and an earlytermination codon at codon 172. This frame-shift is identical to thatwhich we predicted from our Δ2,3 isoform, and it appears that thesevariants are in fact the same, despite the different designations (Δ2,3versus Δ3,4). It appears that this discrepancy has arisen because Zuo etal consider the 5′ UTR as exon 1, whereas we have followed theconvention in the FoxP3 literature (11, 14, 15, 23) to consider thefirst translated region as exon 1. Nevertheless, it appears that thissplice variant is expressed in a wide range of cancers includingmelanoma (FIG. 4), breast cancer (FIG. 4, and reference (27)) and others(FIG. 5).

In contrast to breast cancer, our results suggest that melanoma ischaracterized by up-regulation of FoxP3 rather than down-regulation.First, FoxP3 expression was expressed at readily detectable levels bythe majority of melanoma cell lines, in contrast to breast cancer celllines which frequently lacked FoxP3 expression (reference (27), and FIG.5). In addition, normal epidermal melanocytes lacked significant FoxP3expression but the malignant counterpart (melanoma cells) clearlyexpressed FoxP3. Normal breast epithelium, in contrast, expresses FoxP3constitutively and expression is lost or down-regulated in breast cancertissue.

Recent studies into the epigenetic regulation of FOXP3 have revealedthat gene expression is normally repressed by methylation of a CpG-richelement in the 5′-UTR. In Tregs, however, this region is almostcompletely demethylated, leading to stable, heritable FOXP3 geneexpression (28). The importance of such epigenetic control is revealedfollowing treatment of NK cells with the demethylating agent 5-aza-2′deoxycytidine, which allows these cells to abnormally express FoxP3 inresponse to IL-2 (29). Interestingly, aberrant methylation anddemethylation are common events in melanoma, and many melanoma antigens,including the MAGE and cancer testis (CT) antigen families, areexpressed following promoter demethylation (30, 31). Together, theseobservations raise the possibility that deregulated demethylase activityin melanoma cells results in the coordinate induction of tumor antigenand FoxP3 expression.

Given the established role for FoxP3 in directing Treg activity,up-regulated FoxP3 expression in melanoma cells may endow them withTreg-like activity and enable FoxP3+ melanoma cells to resist immuneattack. In support of this hypothesis, FoxP3-expressing melanoma cellscould effectively suppress T cell proliferation, with almost completeinhibition being observed when melanoma cells outnumber T cells 2:1, asituation that is very likely to occur within the tumormicroenvironment. Interestingly, the single FoxP3+ breast cancer cellline we could identify was also strongly suppressive.

Tumor cells are well known to have immunosuppressive activity. Theseactivities include production of immunoregulatory cytokines, preventionof DC maturation, generation of Treg, and many others (6, 32, 33).However, until now, very few studies have shown a direct effect of tumorcells on inhibiting T cell activation and expansion (34). Our resultsshow that the ability to suppress T cell proliferation is common amongstFoxP3-expressing tumor cell lines. In keeping with our results, Hinz etal (42) found that FoxP3+ pancreatic carcinoma cell lines could alsosuppress T cell proliferation. Importantly, these authors also used anRNA interference approach to demonstrate that FoxP3 was at leastpartially responsible for the suppression mediated by tumor cells.Interestingly, however, we have observed that some tumor cell linesexpressing only borderline levels of FoxP3 could also effectivelysuppress T cell proliferation (data not shown), supporting the view thattumor cells possess additional immunosuppressive mechanisms that areindependent of FoxP3. In future studies, it will be important todirectly assess what contribution FoxP3 makes to the observedimmunosuppressive activity of tumor cells; for example, by using RNAiapproaches.

The function of FoxP3 in cancer may depend on the nature of the tumor.In breast cancer, loss of FoxP3 expression is thought to contribute totumorigenesis by allowing enhanced expression of the HER-2/ErbB2oncogene, which plays a key role in breast cancer progression (27). Inthis situation, it is likely that FoxP3 expression would be expected tobe selected against, as any immune-suppressive advantage FoxP3expression could confer will be outweighed by the benefit ofup-regulated expression of a relevant oncogene. In keeping with thisconcept, we found only one out of three breast cancer cell lines to beFoxP3+. In contrast, the HER-2/ErbB2 oncogene is not reported to beinvolved in the pathogenesis of melanoma (35) and therefore there wouldbe no reason for FoxP3 expression to be selected against; to thecontrary, induction of FoxP3 expression may provide a survival advantageto melanoma cells by endowing them with Treg-like activity. An importantquestion for future studies will be to determine if FoxP3 expressioncorrelates with disease progression or has prognostic significance.

In addition to solid tumors, we have provided evidence that B celllymphomas can also aberrantly express FoxP3. Transformation of normal Bcells with the oncogenic virus EBV induced FoxP3 expression, and asub-population of B lymphoma cells from a PTLD patient were FoxP3⁺. Forseveral years, it has been recognized that adult T cellleukemia/lymphoma is frequently associated with FoxP3 expression (36).The common interpretation of this observation is that these malignanciesare derived from the Treg lineage. However, our observation of de novoFoxP3 induction in malignant B cells raises the possibility that aproportion of FoxP3⁺ T cell leukemias are in fact derived fromnon-regulatory T cells that have begun expressing FoxP3 duringtumorigenesis.

Our data raise the possibility that FoxP3 may be a potential tumorantigen that can be targeted by vaccination. Although FoxP3 is a selfantigen, it is not expressed in thymic epithelium (26) and tolerance tothis antigen is apparently very limited, as T cell responses againstFoxP3 could be readily induced following vaccination of mice (37). Apotential concern in targeting FoxP3 as a tumor antigen is thepossibility that Treg would also be targeted for destruction,potentially leading to autoimmunity. Of note, however, is ourobservation that a number of tumor cell lines expressed a FOXP3 mRNAisoform lacking exons 2 and 3 which was not detectable in Treg. Thisisoform is predicted to encode a novel protein which is approximatelyhalf the size of FoxP3 and—due to a translation frame-shift—includes a103aa sequence that has very limited homology to FOXP3 any other knownprotein sequence. Targeting this protein by vaccination would allow thegeneration of T cells that recognize tumor but not Treg, therebyeliminating the possibility of autoimmune complications. Interestingly,Zuo et al also detected novel FOXP3 mRNA variants in breast cancercells, one of which appears to be identical to the Δ2,3 variant(although these authors refer to this variant as Δ 3,4; presumablybecause they consider the 5′ UTR as exon 1). Therefore, alternativesplicing of the FOXP3 gene appears to be a common theme in cancer.

This study demonstrates, for the first time, that FoxP3 is expressed inmelanoma cells both directly ex vivo and after culture in vitro. Thus,FoxP3 expression by melanoma cells is neither a culture artifact nor atransient phenomenon. We have also demonstrated FoxP3 expression in Bcells that have been transformed with EBV in vitro and in vivo, as wellas a variety of other tumor cell lines, although further investigationis required to determine if each of these tumors also expresses FoxP3 invivo. These observations suggest a re-interpretation of previous studiesin which Treg prevalence in tumors was investigated by measuring FOXP3transcripts in the tumor tissue, as some of these transcripts may haveoriginated from the tumor cells themselves, not from Treg. Clearly,FoxP3 expression and function can no longer be considered to berestricted to the T cell lineage—but may instead play a wider role inbiology; for example, by endowing tumor cells with immune suppressiveactivity. These observations raise the possibility of enhancing tumorimmunogenicity by knocking down FoxP3 expression (for example, using RNAinterference) or, alternatively, by vaccinating against the FoxP3 Δ2,3isoform.

Western blotting and T cell screening data confirm that the FoxP3 Δ2,3isoform is expressed and a suitable target for immunological therapeuticintervention. Western blot data demonstrated expression of the FoxP3Δ2,3 isoform using a polyclonal antibody raised against theframe-shifted region. Results from screening a patient for T cellsspecific for the FoxP3 Δ2,3 isoform also indicate that the FoxP3 Δ2,3isoform is expressed and generates a CD4+ and CD8+ T cell immuneresponse. A series of overlapping peptides were synthesized covering theentire sequence of the variant and were used to stimulate patient PBMC.It is interesting to note that no responses were detected in the first70 amino acids of the protein, which is the portion encoded by exon 1and is identical to native FoxP3. In contrast, the region between aminoacids 97-171 appeared to have many epitopes. This is the portion of theprotein generated from the alternative reading frame, and has acompletely different sequence as compared to FoxP3. These resultssupport the concept that this variant can act as a tumour antigen, andalso provide indirect evidence that the variant is produced as aprotein, as otherwise it would not be possible to generate an immuneresponse to it.

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Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

All references disclosed herein are incorporated by reference in theirentirety.

1. An isolated nucleic acid molecule selected from the group consistingof: (a) complements of nucleic acid molecules that hybridize under highstringency conditions to a second nucleic acid molecule comprising anucleotide sequence set forth as SEQ ID NO:6, foxp3 (SEQ ID NO:1)lacking exons 2 and 3, or foxp3 exons 1 and 4 joined together, (b)nucleic acid molecules that differ from the nucleic acid molecules of(a) in codon sequence due to the degeneracy of the genetic code, and (c)full-length complements of (a) or (b); or a nucleotide sequence that isat least about 90% identical to a nucleotide sequence set forth as SEQID NO:6, foxp3 (SEQ ID NO:1) lacking exons 2 and 3, or foxp3 exons 1 and4 joined together, or a full-length complement thereof. 2-12. (canceled)13. A composition comprising the isolated nucleic acid molecule of claim1 and a carrier.
 14. A composition comprising the isolated nucleic acidmolecule of claim 1 attached to a solid substrate.
 15. A kit comprising:one or more nucleic acid molecules that hybridize under high stringencyconditions to the isolated nucleic acid molecule of claim 1, optionallywherein the one or more nucleic acid molecules are detectably labeledand/or wherein the one or more nucleic acid molecules consist of a firstprimer and a second primer, wherein the first primer and the secondprimer are constructed and arranged to selectively amplify at least aportion of a nucleic acid molecule that comprises a nucleotide sequenceset forth as SEQ ID NO:6, foxp3 (SEQ ID NO:1) lacking exons 2 and 3, orfoxp3 exons 1 and 4 joined together. 16-17. (canceled)
 18. An expressionvector comprising the isolated nucleic acid molecule of claim 1 operablylinked to a promoter.
 19. An isolated host cell transformed ortransfected with the expression vector of claim
 18. 20. An isolatedpolypeptide encoded by the isolated nucleic acid molecule of claim 1 orthat comprises the amino acid sequence of SEQ ID NO:11.
 21. An isolatedantibody or antigen-binding fragment thereof that selectively binds tothe isolated polypeptide of claim 20, optionally wherein the antibody isa monoclonal antibody, a human antibody, a domain antibody, a humanizedantibody, a single chain antibody or a chimeric antibody, and/or whereinthe antibody fragment is a F(ab′)₂, Fab, Fd, or Fv fragment. 22-23.(canceled)
 24. A composition comprising the isolated antibody orantigen-binding fragment of claim 21 and a carrier.
 25. A kit comprisingthe isolated antibody or antigen-binding fragment of claim
 21. 26. AsiRNA molecule that selectively targets SEQ ID NO:6, foxp3 (SEQ ID NO:1)lacking exons 2 and 3, or a nucleic acid molecule comprising foxp3 exons1 and 4 joined together.
 27. A method for diagnosing cancer in a subjectcomprising obtaining a biological sample from the subject, anddetermining the expression in the biological sample of a FoxP3polypeptide or a nucleic acid molecule that encodes the FoxP3polypeptide, wherein the nucleic acid molecule comprises SEQ ID NO:1, ora nucleotide sequence that is at least 90% identical to the nucleotidesequence of SEQ ID NO:1, wherein the cancer is not pancreatic carcinomaand wherein the expression in the biological sample of the polypeptideor the nucleic acid molecule that encodes it is indicative of thesubject having cancer, optionally wherein the biological sample is freeof regulatory T cells (T_(reg); CD4+CD25+FOXP3+).
 28. (canceled)
 29. Themethod of claim 27, wherein the step of determining the expression ofthe polypeptide or the nucleic acid molecule that encodes thepolypeptide comprises contacting the biological sample with an agentthat selectively binds to the polypeptide or the nucleic acid moleculethat encodes the polypeptide.
 30. The method of claim 29, wherein theagent is a nucleic acid probe or a nucleic acid primer, optionallywherein the expression of the nucleic acid molecule is determined bynucleic acid hybridization using the nucleic acid probe or nucleic acidamplification using the nucleic acid primer, preferably wherein thenucleic acid amplification is real-time RT-PCR or RT-PCR, or wherein thenucleic acid hybridization is performed using a nucleic acid microarraycontaining the nucleic acid probe, optionally wherein the samplecomprises tissue, cells, and/or blood. 31-33. (canceled)
 34. The methodof claim 29, wherein the agent is a polypeptide, optionally wherein thepolypeptide is an antibody or antigen-binding fragment thereof,preferably wherein the antibody is a monoclonal antibody, or wherein theantigen-binding fragment is a F(ab′)₂, Fab, Fd, or Fv fragment,optionally wherein the antibody or antigen-binding fragment is labeledwith a detectable label, preferably wherein the detectable label is afluorescent or radioactive label, optionally wherein the samplecomprises tissue, cells, and/or blood. 35-40. (canceled)
 41. A methodfor diagnosing cancer in a subject comprising obtaining a biologicalsample from the subject, and determining the expression in thebiological sample of a FoxP3 polypeptide or a nucleic acid molecule thatencodes the FoxP3 polypeptide, wherein the nucleic acid moleculecomprises (1) SEQ ID NO:6, foxp3 (SEQ ID NO:1) lacking exons 2 and 3, ora nucleic acid molecule comprising foxp3 exons 1 and 4 joined together,or (2) a nucleotide sequence that is at least 90% identical to thenucleotide sequence of (1), wherein the expression in the biologicalsample of the polypeptide or the nucleic acid molecule that encodes itis indicative of the subject having cancer, optionally wherein thebiological sample is free of regulatory T cells (T_(reg);CD4+CD25+FOXP3+).
 42. (canceled)
 43. The method of claim 41, wherein thestep of determining the expression of the polypeptide or the nucleicacid molecule that encodes the polypeptide comprises contacting thebiological sample with an agent that selectively binds to thepolypeptide or the nucleic acid molecule that encodes the polypeptide.44. The method of claim 43, wherein the agent is a nucleic acid probe ora nucleic acid primer, optionally wherein the expression of the nucleicacid molecule is determined by nucleic acid hybridization using thenucleic acid probe or nucleic acid amplification using the nucleic acidprimer, preferably wherein the nucleic acid amplification is real-timeRT-PCR or RT-PCR, or wherein the nucleic acid hybridization is performedusing a nucleic acid microarray containing the nucleic acid probe,optionally wherein the sample comprises tissue, cells, and/or blood.45-47. (canceled)
 48. The method of claim 43, wherein the agent is apolypeptide, optionally wherein the polypeptide is an antibody orantigen-binding fragment thereof, preferably wherein the antibody is amonoclonal antibody, or wherein the antigen-binding fragment is aF(ab′)₂, Fab, Fd, or Fv fragment, optionally wherein the antibody orantigen-binding fragment is labeled with a detectable label, preferablywherein the detectable label is a fluorescent or radioactive label,optionally wherein the sample comprises tissue, cells, and/or blood.49-94. (canceled)